System and method for automated digital polymerase chain reaction

Abstract

Systems and methods for automated digital polymerase chain reactions are described herein. A method of performing an automated digital polymerase chain reaction (PCR) may include receiving a sample in a sample tube within a sample tube holder of an automated digital PCR system. The automated digital PCR system may include a multi-channel pipettor, a heater that may thermally cycle a sample in a PCR cartridge, and an imager. The method may include: performing a pipetting operation with the multi-channel pipettor to transfer a portion of the sample into a PCR cartridge; carrying out thermal circulation on the sample in the PCR cylinder by using the heater; and imaging the sample in the PCR cartridge by using the imager.

Description

[0001] Cross-reference to related applications

[0002] This application claims the benefit of U.S. Provisional Application No. 63 / 343,485, filed on May 18, 2022, and entitled “Systems And Methods For Automated Sample Preparation, Assay Preparation, Digital Assays, And Other Analyses,” and U.S. Provisional Application No. 63 / 421,928, filed on November 2, 2022, and entitled “Systems And Method For Automated Digital Polymerase Chain Reaction,” the entire contents of each of which are hereby incorporated herein by reference. Background Art

[0003] The polymerase chain reaction (PCR) is widely used to quickly make large numbers of copies of a specific DNA sample. With PCR, very small DNA samples can be amplified to large enough quantities to be studied in detail.

[0004] Droplet digital PCR (ddPCR) divides the PCR sample into partitions (e.g., water-in-oil droplets). See, for example, Hindson et al., 2011, Anal. Chem. 83:8604-8610; Pinheiro et al., 2012, Anal. Chem. 84:1003-1011. The droplets support PCR amplification of the template molecule (if present), and use reagents that can specifically generate signals from the target amplicon (i.e., the amplicon from the target sequence). After PCR, the signal from each droplet is read to determine the number of positive droplets for each target amplified in the original sample (e.g., including partitions with multiple different targets and parts with only a single or no target signal). Digital PCR is a refinement of conventional PCR and can be more accurate than conventional PCR. However, operator error can reduce the accuracy of digital PCR. Summary of the invention

[0005] Aspects of the present disclosure relate to systems and methods for automated digital polymerase chain reactions. One aspect relates to a method for performing an automated digital polymerase chain reaction (PCR). The method includes receiving a sample in a sample tube within a sample tube holder of an automated digital PCR system. In some embodiments, the automated digital PCR system includes a multichannel pipette, a heater that can perform thermal cycling on a sample in a PCR cartridge, and an imager. The method may include: performing a pipetting operation with the multichannel pipette to transfer a portion of the sample to a PCR cartridge; thermal cycling the sample in the PCR cartridge with the heater; and imaging the sample in the PCR cartridge with the imager.

[0006] In some embodiments, the digital PCR system further comprises an assay strip that may include at least one well. The method further comprises generating a final reaction mixture in at least one well of the assay strip. In some embodiments, at least one of the pipetting operations transfers the final reaction mixture from at least one well of the assay strip to a PCR cartridge. In some embodiments, more than 50% of the DNA contained in at least one well of the assay strip is contained in the PCR cartridge. In some embodiments, performing the pipetting operation with the multichannel pipette comprises transferring multiple samples to the same PCR cartridge simultaneously.

[0007] In some embodiments, the automated digital PCR system includes a baffle having a position for receiving a cartridge. In some embodiments, one of the positions for receiving a cartridge may include a sample tube holder. In some embodiments, a pipette may be above and move across the baffle. In some embodiments, the pipette may include at least one pipette tip and a drip tray that may move from a first position below the at least one pipette tip to a second position.

[0008] In some embodiments, performing a pipetting operation includes moving the drip tray from the first position to the second position prior to moving the pipette across the partition. In some embodiments, the drip tray remains in the second position until the pipette is positioned for aspiration or dispensing. In some embodiments, the pipette includes a plurality of suction cups coupled to the drip tray. In some embodiments, the suction cup is movable from a first position to a second position. In some embodiments, the suction cup is retracted in a first position and unfolded in a second position. In some embodiments, when the suction cup is unfolded, the suction cup can pick up and move the PCR cartridge.

[0009] In some embodiments, the method includes preparing the sample for thermal cycling. In some embodiments, preparing the sample for thermal cycling includes lysing the sample, binding the lysed sample to magnetic beads, and pre-concentrating the sample in a pipette tip. In some embodiments, pre-concentrating the sample in the pipette tip includes: aspirating a portion of the sample into the pipette tip, wherein nucleic acids in the sample bind to magnetic beads; positioning the pipette tip adjacent to a magnet that can attract the magnetic beads; and dispensing a portion of the sample while the pipette tip is adjacent to the magnet.

[0010] One aspect relates to a system for performing an automated digital polymerase chain reaction (PCR). The system includes a multichannel pipette; a heater that can perform thermal cycling on a sample in a PCR cartridge; an imager; and a processor that is communicatively coupled to each of the pipette, the heater, and the imager. In some embodiments, the processor can control the operation of each of the pipette, the heater, and the imager to perform digital PCR. In some embodiments, the processor can receive an indication of receiving a sample in a sample tube within a sample tube holder of the automated digital PCR system; perform a pipetting operation with the pipette to transfer a portion of the sample to a PCR cartridge; perform thermal cycling on the sample in the PCR cartridge with the heater; and image the sample in the PCR cartridge with the imager.

[0011] In some embodiments, the system further includes a baffle having a position for receiving the cartridge. In some embodiments, one of the positions for receiving the cartridge may include a sample tube holder. In some embodiments, the pipette may be above the baffle and move across the baffle. In some embodiments, the pipette may include at least one pipette tip and a drip tray that may move from a first position below the at least one pipette tip to a second position.

[0012] In some embodiments, performing a pipetting operation includes moving the drip tray from the first position to the second position prior to moving the pipette across the partition. In some embodiments, the drip tray remains in the second position until the pipette is positioned for aspiration or dispensing. In some embodiments, the pipette includes a plurality of suction cups coupled to the drip tray. In some embodiments, the suction cup is movable from a first position to a second position. In some embodiments, the suction cup is retracted in a first position and unfolded in a second position. In some embodiments, when the suction cup is unfolded, the suction cup can pick up and move the PCR cartridge.

[0013] In some embodiments, the processor may further control preparing the sample for thermal cycling. In some embodiments, preparing the sample for thermal cycling includes lysing the sample, binding the lysed sample to magnetic beads, and pre-concentrating the sample in a pipette tip. In some embodiments, pre-concentrating the sample in the pipette tip includes: aspirating a portion of the sample into the pipette tip, wherein nucleic acids in the sample bind to magnetic beads; positioning the pipette tip adjacent to a magnet that can attract the magnetic beads; and dispensing a portion of the sample while the pipette tip is adjacent to the magnet.

[0014] One aspect relates to a method for automatic image normalization. The method includes generating an image of an irradiated area including a plurality of partitions on a PCR chip, each of the partitions containing an assay mixture, the image including a plurality of pixels. The method includes: using a machine learning model to identify pixels from the image as belonging to a valid partition or belonging to a background; dividing the image into a plurality of segments, each segment containing a plurality of pixels; generating an average brightness value for at least some of the partitions in each segment; generating a normalized value for each segment, the normalized value being based at least in part on the average brightness value of the segment; normalizing the pixel values ​​in the segment according to the normalized value for each segment; and analyzing the image based on the normalized pixel values ​​to determine the presence or absence of at least one target.

[0015] In some embodiments, each of the plurality of segments contains the same number of pixels. In some embodiments, the method comprises: for each partition in each segment, identifying an image portion corresponding to the partition; and identifying a brightness value for each of the image portions. In some embodiments, the method comprises identifying a brightness value corresponding to a negative partition in each of the segments. In some embodiments, a negative partition is a partition with a low signal captured in an image. In some embodiments, generating the average brightness value of at least some of the partitions in each segment comprises generating an average negative partition brightness value for the negative partitions in each segment.

[0016] In some embodiments, the method includes comparing the average negative partition brightness value for each of the segments; and identifying a minimum average negative partition brightness value. In some embodiments, generating the normalized value for each segment includes, for each segment, retrieving the negative partition brightness value for the segment; and dividing the negative partition brightness value by the minimum average negative partition brightness value. In some embodiments, normalizing the pixel values ​​in the segment according to the normalized value for each segment includes, for each pixel value in the segment: retrieving the pixel value; and dividing the pixel value by the normalized value.

[0017] In some embodiments, identifying pixels from the image as belonging to a valid partition or to the background using the machine learning model includes: selecting pixels; predicting the probability of the selected pixels belonging to a partition using the machine learning model; identifying those one or more pixels as belonging to a candidate partition based on a comparison of the predicted probability of one or more pixels with a threshold; comparing each candidate partition with a series of thresholds; and identifying the candidate partition as a partition when the size of the candidate partition is within an acceptable range defined by the series of thresholds.

[0018] One aspect relates to a system for performing image normalization as part of an automated digital polymerase chain reaction (PCR). The system includes a multichannel pipette; a heater that can perform thermal cycling on a sample in a PCR cartridge; an imager; and a processor that is communicatively coupled to each of the pipette, the heater, and the imager. In some embodiments, the processor can generate an image of an irradiated area including a plurality of partitions, the image including a plurality of pixels. The processor can use a machine learning model to identify pixels from the image as belonging to a valid partition or to background; divide the image into a plurality of segments, each segment containing a plurality of pixels; generate an average brightness value for at least some of the partitions in each segment; generate a normalized value for each segment, the normalized value being based at least in part on the average brightness value of the segment; normalize the pixel values ​​in the segment according to the normalized value for each segment; and analyze the image based on the normalized pixel values ​​to determine the presence or absence of at least one target.

[0019] In some embodiments, each of the plurality of segments contains the same number of pixels. In some embodiments, the processor may, for each partition in each segment, identify an image portion corresponding to the partition; and identify a brightness value for each of the image portions. In some embodiments, the processor may identify a brightness value corresponding to a negative partition in each of the segments.

[0020] In some embodiments, each negative partition has a low signal captured in the image. In some embodiments, generating the average brightness value for at least some of the partitions in each segment includes generating an average negative partition brightness value for the negative partitions in each segment. In some embodiments, the processor may further compare the average negative partition brightness value for each of the segments; and identify a minimum average negative partition brightness value.

[0021] In some embodiments, generating the normalized value for each segment includes, for each segment, retrieving the negative partition brightness value for the segment; and dividing the negative partition brightness value by the minimum average negative partition brightness value. In some embodiments, normalizing the pixel values ​​in the segment according to the normalized value for each segment includes, for each pixel value in the segment: retrieving the pixel value; and dividing the pixel value by the normalized value.

[0022] In some embodiments, identifying pixels from the image as belonging to a valid partition or to the background using the machine learning model includes: selecting pixels; predicting the probability of the selected pixels belonging to a partition using the machine learning model; identifying those one or more pixels as belonging to a candidate partition based on a comparison of the predicted probability of one or more pixels with a threshold; comparing each candidate partition with a series of thresholds; and identifying the candidate partition as a partition when the size of the candidate partition is within an acceptable range defined by the series of thresholds.

[0023] One aspect relates to a method for detecting monolayer droplets on a PCR chip. The method includes: generating droplets of a sample on a substrate; generating an image of multiple droplets on the substrate; for each droplet, determining whether the droplet is a monolayer using an artificial intelligence classifier; and analyzing a portion of the image containing the monolayer droplets to determine whether at least one target is present in each droplet.

[0024] In some embodiments, the method includes: receiving the sample; and preparing the sample for PCR. In some embodiments, each of the droplets can have a volume between about 10 picoliters and about 1000 picoliters. In some embodiments, generating droplets of the sample on the substrate includes generating at least 500,000 droplets of the sample on the substrate.

[0025] In some embodiments, the image includes a plurality of pixels. In some embodiments, the method further includes identifying pixels from the image as belonging to valid droplets or belonging to background using a machine learning model. In some embodiments, for each droplet, determining whether the droplet is a monolayer using the artificial intelligence classifier includes: ingesting the image of the droplet of the sample into the artificial intelligence classifier; and receiving an output from the artificial intelligence classifier, the output identifying a probability of each droplet being a monolayer droplet. In some embodiments, for each droplet, determining whether the droplet is a monolayer using the artificial intelligence classifier further includes, for each droplet, comparing the output of the artificial intelligence classifier to a threshold.

[0026] In some embodiments, the method includes: identifying a portion of the image containing non-monolayer droplets; identifying a portion containing monolayer droplets; and excluding the identified portion from the sample analysis. In some embodiments, the method includes: determining a total size of the portion containing monolayer droplets; and comparing the total size of the portion containing monolayer droplets to a threshold. In some embodiments, the total size is determined by combining the size of each portion in the portion containing monolayer droplets. In some embodiments, when the total size of the portion containing monolayer droplets is less than the threshold, the method includes generating an alarm indicating an invalid test result.

[0027] One aspect relates to a system for performing monolayer detection as part of an automated digital polymerase chain reaction (PCR). The system includes a substrate; a multichannel pipette; an imager; and a processor communicatively coupled to each of the pipette, the heater, and the imager. In some embodiments, the processor can generate droplets of a sample on the substrate with the pipette; generate an image of a plurality of droplets on the substrate with the imager; for each droplet, determine whether the droplet is a monolayer with an artificial intelligence classifier; and analyze a portion of the image containing the monolayer droplets to determine whether at least one target is present in each droplet.

[0028] In some embodiments, the processor may receive an indication to receive a sample; and prepare the sample for PCR. In some embodiments, each of the droplets may have a volume between about 10 picoliters and about 1000 picoliters. In some embodiments, generating droplets of the sample on the substrate comprises generating at least 500,000 droplets of the sample on the substrate.

[0029] In some embodiments, the image includes a plurality of pixels. In some embodiments, the processor may use a machine learning model to identify pixels from the image as belonging to valid droplets or belonging to background. In some embodiments, for each droplet, determining with the artificial intelligence classifier whether the droplet is a monolayer comprises: ingesting the image of the droplet of the sample into the artificial intelligence classifier; and receiving an output from the artificial intelligence classifier, the output identifying the probability of each droplet being a monolayer droplet. In some embodiments, for each droplet, determining with the artificial intelligence classifier whether the droplet is a monolayer further comprises, for each droplet, comparing the output of the artificial intelligence classifier to a threshold. In some embodiments, the processor may identify portions of the image containing non-monolayer droplets; identify portions containing monolayer droplets; and exclude the identified portions from sample analysis.

[0030] In some embodiments, the processor may determine a total size of the portion containing a monolayer of droplets; and compare the total size of the portion containing a monolayer of droplets to a threshold. In some embodiments, the total size is determined by combining the size of each portion in the portion containing a monolayer of droplets. In some embodiments, when the total size of the portion containing a monolayer of droplets is less than the threshold, the processor may generate an alarm indicating an invalid test result.

[0031] One aspect relates to a method for pre-concentrating nucleic acids in a sample in the tip of a pipette of an apparatus for performing an automated digital polymerase chain reaction (PCR). The method includes receiving a first sample in a sample tube in a sample tube holder of an automated digital PCR system. The automated digital PCR system includes a multi-channel pipette, a heater that can perform thermal cycling on samples in a PCR cartridge, and an imager. The method includes aspirating a first sample including nucleic acids into a pipette tip of a pipette. In some embodiments, nucleic acids in the first sample are bound to magnetic beads. The method includes positioning the pipette tip of the pipette adjacent to a magnet, whereby the magnetic beads are attracted to the magnet. The method includes pre-concentrating the nucleic acids bound to the magnetic beads of the first sample in the pipette tip by dispensing a portion of the first sample when the pipette tip is adjacent to the magnet. In some embodiments, magnetic beads are attracted to the magnet to keep the magnetic beads in an undispensed portion of the first sample. The method includes: concentrating the nucleic acids of the first sample bound to the magnetic beads in the wells of a magnet plate; thermally cycling the nucleic acids of the first sample in the PCR cartridge with the heater; and imaging the nucleic acids of the first sample in the PCR cartridge with the imager.

[0032] In some embodiments, the magnet can be a magnet located on one side of a sample tube. In some embodiments, the allocated portion of the first sample is allocated in the sample tube. In some embodiments, the pipette tip includes a proximal end and a distal end. In some embodiments, the pipette tip is positioned adjacent to the magnet so that the magnet is located between the proximal end and the distal end of the pipette tip.

[0033] In some embodiments, the portion of the first sample dispensed when the pipette tip is adjacent to the magnet may account for approximately 90% of the first sample aspirated. In some embodiments, the portion of the first sample dispensed when the pipette tip is adjacent to the magnet may account for approximately 50% to approximately 95% of the first sample aspirated. In some embodiments, when dispensing the portion of the first sample, the pipette tip is positioned adjacent to the magnet so that the distal end of the pipette tip extends below the magnet and into the sample tube and so that the first sample in the pipette extends above the magnet. In some embodiments, after completing the dispensing of the portion of the first sample, the first sample extends above the magnet.

[0034] In some embodiments, the method includes dispensing the remaining portion of the first sample into a well in a magnet plate, the well in the magnet plate being exposed to a magnetic field that attracts the magnetic beads and holds the magnetic beads within the well. In some embodiments, the method includes concentrating the magnetic beads of the second sample in the pipette tip by dispensing a portion of the second sample while the pipette tip is adjacent to the magnet. In some embodiments, attracting the magnetic beads to the magnet holds the magnetic beads in an undispensed portion of the second sample. In some embodiments, the method includes dispensing the remaining portion of the second sample into the well in the magnet plate.

[0035] In some embodiments, the method includes aspirating the first sample and the remaining portion of the second sample from the wells in the magnet plate, the magnetic field retaining the magnetic beads within the wells.

[0036] One aspect relates to a system for pre-concentrating nucleic acids in an automated digital polymerase chain reaction (PCR). The system includes a multi-channel pipette; a sample tube; a magnet plate including a plurality of holes; a partition including a position for receiving the sample tube and the magnet plate; and a processor communicatively coupled to the pipette. The processor can control the operation of each of the pipette, the heater, and the imager to perform digital PCR. The processor can receive an indication to receive a first sample in the sample tube, the sample tube being located within the position of the partition for receiving the sample tube; aspirating a first sample including nucleic acid into a pipette tip of the pipette with the pipette, the nucleic acid in the first sample being bound to magnetic beads; positioning the pipette tip of the pipette adjacent to a magnet, whereby the magnetic beads are attracted to the magnet; concentrating the magnetic beads of the first sample in the pipette tip by dispensing a portion of the first sample when the pipette tip is adjacent to the magnet, the attracting of the magnetic beads to the magnet retaining the magnetic beads in an undispensed portion of the first sample; thermally cycling the nucleic acid of the first sample in the PCR cartridge with the heater; and imaging the nucleic acid of the first sample in the PCR cartridge with the imager.

[0037] In some embodiments, the magnet can be a magnet located on one side of a sample tube. In some embodiments, the allocated portion of the first sample is allocated in the sample tube. In some embodiments, the pipette tip includes a proximal end and a distal end. In some embodiments, the pipette tip is positioned adjacent to the magnet so that the magnet is located between the proximal end and the distal end of the pipette tip. In some embodiments, the portion of the first sample allocated when the pipette tip is adjacent to the magnet can account for approximately 90% of the first sample aspirated. In some embodiments, the portion of the first sample allocated when the pipette tip is adjacent to the magnet can account for approximately 50% to approximately 95% of the first sample aspirated.

[0038] In some embodiments, when dispensing the portion of the first sample, the pipette tip is positioned adjacent to the magnet so that the distal end of the pipette tip extends below the magnet and into the sample tube and so that the first sample in the pipette extends above the magnet. In some embodiments, after completing the dispensing of the portion of the first sample, the first sample extends above the magnet. In some embodiments, the processor may dispense the remaining portion of the first sample into one of the plurality of wells in the magnet plate, the one of the plurality of wells in the magnet plate being exposed to a magnetic field that attracts the magnetic beads and holds the magnetic beads within the one of the plurality of wells. In some embodiments, the processor may concentrate the magnetic beads of the second sample in the pipette tip by dispensing a portion of the second sample while the pipette tip is adjacent to the magnet. In some embodiments, attracting the magnetic beads to the magnet holds the magnetic beads in the undispensed portion of the second sample. In some embodiments, the processor may dispense the remaining portion of the second sample into the one of the plurality of wells in the magnet plate.

[0039] In some embodiments, the processor can aspirate the first sample and the remaining portion of the second sample from the one of the plurality of wells in the magnet plate with the pipette, wherein the magnetic field holds the magnetic beads within the one of the plurality of wells.

[0040] One aspect relates to a system for automating digital polymerase chain reaction (PCR). The system includes a housing; a partition including a position for receiving a cartridge used in the digital PCR, the partition being located within the housing; and a multichannel pipette, the multichannel pipette being movable above and across the partition. The multichannel pipette may include a pipette body, the pipette body being movable above and across the partition; and a pipette assembly, the pipette assembly being coupled to the pipette body and being movable relative to the pipette body. In some embodiments, the pipette assembly may be movable from a first position at a first vertical distance relative to the partition to a second position at a second vertical distance relative to the partition. The pipette assembly may include a plurality of dispensing heads, each of which may be engaged with a pipette tip in cooperation and fluidically coupled to the pipette tip; and a drip tray assembly, the drip tray assembly being movable relative to both the pipette body and the pipette assembly. In some embodiments, the drip tray can be automatically deployed between the pipette tip coupled to one of the dispense heads and the septum.

[0041] In some embodiments, the drip tray may include a storage area that can accommodate an absorbent pad. In some embodiments, the absorbent pad is disposable. In some embodiments, the pipette assembly may include eight dispensing heads. In some embodiments, the system includes a z-motor coupled to the pipette assembly. In some embodiments, the pipette assembly may be moved relative to the pipette body by the z-motor.

[0042] In some embodiments, the system includes a drip tray z-motor. In some embodiments, the drip tray assembly is movable relative to both the pipette body and the pipette assembly by the drip tray z-motor. In some embodiments, the drip tray assembly includes: a vertical displacement member; and a drip tray pivotally coupled to a bottom end of the vertical displacement member. In some embodiments, the drip tray assembly further includes an actuation member having a first end and a second end. In some embodiments, the first end of the actuation member is pivotally coupled to the drip tray. In some embodiments, the second end of the actuation member is slidably coupled to the drip tray assembly.

[0043] In some embodiments, when the drip tray assembly is moved to a deployed position, the actuation member can deploy the drip tray between the pipette tip coupled to the dispensing head and the diaphragm. In some embodiments, the deployed position is defined relative to a pipette assembly.

[0044] In some embodiments, the drip tray assembly further includes a plurality of suction cups. In some embodiments, the suction cups are coupled to the vertical displacement member. In some embodiments, the suction cups are deployed when the drip tray is deployed. In some embodiments, when the suction cups are deployed, at least a portion of the suction cups extend below the drip tray. In some embodiments, the system includes a suction pump that is fluidly connected to the suction cups and can create a vacuum in the suction cups. In some embodiments, the system includes a controller that can control the operation of the z motor, the drip tray z motor, and the suction pump.

[0045] One aspect relates to a method for performing an automated digital polymerase chain reaction (PCR). The method includes: receiving a sample tube in a sample tube holder in a bulkhead of an automated digital PCR system; moving a pipette tip coupled to a pipette toward the bulkhead to insert the pipette tip into the sample tube; aspirating a portion of the sample from the sample tube into the pipette tip coupled to the pipette; moving the pipette tip away from the bulkhead to retract the pipette tip from the sample tube; automatically deploying a drop tray between the pipette tip and the bulkhead; creating a plurality of partitions on a PCR chip, wherein at least a portion of the sample is contained in the pipette tip; and thermal cycling and imaging the plurality of partitions.

[0046] In some embodiments, the pipette includes: a pipette body that is movable above and across the partition; and a pipette assembly that is coupled to the pipette body and movable relative to the pipette body. In some embodiments, the pipette assembly is movable from a first position at a first vertical distance relative to the partition to a second position at a second vertical distance relative to the partition. In some embodiments, the pipette assembly includes a plurality of dispensing heads, each of which can be cooperatively engaged with a pipette tip and fluidly coupled to the pipette tip.

[0047] In some embodiments, the pipette may include a drip tray assembly that is movable relative to both the pipette body and the pipette assembly. In some embodiments, the drip tray assembly may include: a vertical displacement member; and a drip tray that is pivotally coupled to a bottom end of the vertical displacement member. In some embodiments, the drip tray assembly further includes a suction cup coupled to the vertical displacement member.

[0048] In some embodiments, the method further includes: moving the pipette body over and across the partition to over the PCR chip; moving the drip tray assembly toward the partition until the suction cup engages with the PCR chip; controlling the suction pump to generate a vacuum with the suction cup, thereby coupling the PCR chip; while remaining coupled to the PCR chip, moving the drip tray assembly away from the partition; while remaining coupled to the PCR chip, moving the pipette body over and across the partition to over the chip tray; positioning the PCR chip in the chip tray; and controlling the suction pump to release the PCR chip from the suction cup.

[0049] One aspect relates to a method for performing an automated digital polymerase chain reaction (PCR). The method includes: generating a graphical user interface ("GUI") on a screen of a system for automated digital PCR; and receiving, through the GUI, a request for performing an automated digital PCR assay on a sample with the system for automated digital PCR. The method may include generating a first window in the GUI, which may guide a user to set up the system for automated digital PCR. In some embodiments, the first window may include a first pane, the first pane including a first instruction, the first instruction for loading a first consumable into a first position on a partition of the system for automated digital PCR, the partition may include multiple positions. The first window may include a graphical representation of the partition and the multiple positions. In some embodiments, the graphical representation of the partition and the multiple positions indicates the positioning of the first position for housing the first consumable. The method may include: generating a second pane, the second pane including an animated rendering of the system for automated digital PCR and the execution of the first instruction; and upon receiving an indication of completion of the execution of the first instruction for loading the first consumable, updating the graphical representation of the partition to show the first consumable loaded into the first position.

[0050] In some embodiments, the first consumables may include at least one of the following: a sample tube, a reagent cartridge, a tip box, a cleavage and binding plate, a DNA quantitative strip, a PCR cartridge, a PCR cartridge cover, or a magnetic separation plate. In some embodiments, the cleavage and binding plate may be a metal-doped polymer. In some embodiments, the sample tube may be a magnet.

[0051] In some embodiments, the request for performing the automated digital PCR assay identifies an assay type and a reagent for performing the assay. In some embodiments, the first window in the GUI is updated when the user executes a previously provided first instruction. In some embodiments, updating the first window in the GUI includes: updating the first pane to include a second instruction for loading a second consumable into a second position on the bulkhead of the system for automated digital PCR; and updating the graphical representation of the bulkhead and the plurality of positions to indicate the positioning of the second position for housing the second consumable. In some embodiments, updating the first window in the GUI further includes updating the second pane to include the animated rendering of the system for automated digital PCR and the execution of the second instruction.

[0052] In some embodiments, the method includes performing a pre-run check after completing the setup of the system for automated digital PCR. In some embodiments, performing the pre-run check includes determining that each of the consumables used to perform the requested assay is loaded into the correct position of the bulkhead. In some embodiments, performing the pre-run check further includes generating a second window. In some embodiments, the second window includes: an indication of successful completion of the pre-run check; a graphical representation of the bulkhead of the system for automated digital PCR; a graphical representation of each consumable loaded into the bulkhead; and an indication that each of the consumables is successfully loaded into the correct position on the bulkhead. In some embodiments, the method further includes generating a graphical indication of the progress of the requested assay completion. In some embodiments, the method includes, and before generating the first window including the first instruction and the first animation: updating the first pane to include a third instruction for removing one or more consumables from the bulkhead; and updating the second pane to include an animated rendering of the system for automated digital PCR and removing the one or more consumables from the bulkhead according to the third instruction.

[0053] One aspect relates to a system for performing an automated digital polymerase chain reaction (PCR). The system includes: a housing; a partition located within the housing and including a plurality of locations for housing consumables; a multichannel pipette; a screen; and a processor communicatively coupled to each of the pipette and the screen. In some embodiments, the processor may generate a graphical user interface ("GUI") on the screen; receive a request for performing an automated digital PCR assay on a sample through the GUI; and generate a first window in the GUI. In some embodiments, the first window may guide a user to set up the system. In some embodiments, the first window may include a first pane, the first pane including: a first instruction for loading a first consumable into a first position on the partition; and a graphical representation of the partition and the plurality of locations, the graphical representation of the partition and the plurality of locations indicating the positioning of the first position for housing the first consumable. In some embodiments, the first window may include a second pane, the second pane including an animated rendering of the system for automated digital PCR and the execution of the first instruction. The processor may update the graphical representation of the shelf to show the first consumable loaded into the first position upon receiving an indication of completion of execution of the first instruction for loading the first consumable.

[0054] In some embodiments, when the user executes a previously provided first instruction, the first window in the GUI is updated. In some embodiments, updating the first window in the GUI includes: updating the first pane to include a second instruction for loading a second consumable into a second position on the shelf; and updating the graphical representation of the shelf and the plurality of positions to indicate the positioning of the second position for receiving the second consumable. In some embodiments, updating the first window in the GUI further includes updating the second pane to include the animation rendering of the system and the execution of the second instruction.

[0055] In some embodiments, the processor may perform a pre-run check after completing the setup of the system. In some embodiments, performing the pre-run check may include determining that each of the consumables used to perform the requested assay is loaded into a correct position on the bulkhead. In some embodiments, performing the pre-run check further includes generating a second window. In some embodiments, the second window includes: an indication of successful completion of the pre-run check; a graphical representation of the bulkhead of the system; a graphical representation of each consumable loaded into the bulkhead; and an indication that each of the consumables was successfully loaded into the correct position on the bulkhead.

[0056] In some embodiments, the processor may, before generating the first window including the first instructions and the first animation: update the first pane to include third instructions for removing one or more consumables from the partition; and update the second pane to include an animation rendering of the system for automated digital PCR and removing the one or more consumables from the partition according to the third instructions.

[0057] One aspect relates to a method of performing an automated digital droplet polymerase chain reaction (DDPCR). The method includes receiving a sample in a sample tube within a sample tube holder of an automated digital PCR system. In some embodiments, the automated digital PCR system may include a multi-channel pipette, a heater configured to thermally cycle a sample in a PCR cartridge, and an imager. The method may include: generating droplets of a portion of the sample with a droplet generator; performing a pipetting operation with the multi-channel pipette to transfer the droplets to a PCR cartridge; thermally cycling the sample in the PCR cartridge with the heater; and imaging the sample in the PCR cartridge with the imager.

[0058] In some embodiments, the droplet generator may include a substrate and a plurality of droplet generation units, each of the droplet generation units being located on the substrate. In some embodiments, each of the droplet generation units may include: an oil reservoir; a PCR reagent reservoir; and a droplet outlet. In some embodiments, each of the oil reservoir, the PCR reagent reservoir, and the droplet outlet are fluidly coupled via at least one channel extending through the substrate.

[0059] In some embodiments, generating droplets may include: engaging the multi-channel pipette with the droplet outlet of each droplet generating unit of the droplet generator; and applying a vacuum to the droplet outlet of each droplet generating unit of the droplet generator with the multi-channel pipette. In some embodiments, performing the pipetting operation to transfer the droplets into the PCR cartridge includes aspirating the droplets from the droplet outlet of each droplet generating unit of the droplet generator; and dispensing the aspirated droplets into the inlet of the PCR cartridge.

[0060] In some embodiments, the method may include sealing the PCR cartridge, thereby sealing the droplet within the PCR cartridge. In some embodiments, sealing the PCR cartridge may include dispensing a sealant into the inlet of the PCR cartridge. In some embodiments, the sealant may be an ultraviolet ("UV") curable glue. In some embodiments, the method includes curing the UV curable glue prior to thermal cycling the sample in the PCR cartridge.

[0061] In some embodiments, imaging the sample in the PCR cartridge with the imager comprises: moving the imager to a region of interest; illuminating the PCR cartridge; positioning a filter in an optical pathway; and capturing an image of the region of interest. In some embodiments, the region of interest is selected using autofocus.

[0062] One aspect relates to a system for performing an automated digital droplet polymerase chain reaction (DDPCR). The system includes a multichannel pipette; a heater that can perform thermal cycling on a sample in a PCR cartridge; an imager; and a processor that is communicatively coupled to each of the pipette, the heater, and the imager. In some embodiments, the processor can control the operation of each of the pipette, the heater, and the imager to perform digital PCR. In some embodiments, the processor can receive an indication of receiving a sample in a sample tube within a sample tube holder of the automated digital PCR system; generate a droplet containing a portion of the sample with a droplet generator; perform a pipetting operation with the pipette to transfer a portion of the sample to a PCR cartridge; perform thermal cycling on the sample in the PCR cartridge with the heater; and image the sample in the PCR cartridge with the imager.

[0063] In some embodiments, the system further includes a partition including a location for receiving the cartridge. In some embodiments, one of the locations for receiving the cartridge may include a sample tube holder. In some embodiments, the pipette may be movable above and across the partition. In some embodiments, the droplet generator may include a substrate and a plurality of droplet generation units, each of the droplet generation units being located on the substrate. In some embodiments, each of the droplet generation units may include: an oil reservoir; a PCR reagent reservoir; and a droplet outlet. In some embodiments, each of the oil reservoir, the PCR reagent reservoir, and the droplet outlet is fluidly coupled by at least one channel extending through the substrate.

[0064] In some embodiments, generating droplets may include: engaging the multi-channel pipette with the droplet outlet of each droplet generating unit of the droplet generator; and applying a vacuum to the droplet outlet of each droplet generating unit of the droplet generator with the multi-channel pipette. In some embodiments, the pipette may include at least one pipette tip and a drip plate movable from a first position below the at least one pipette tip to a second position.

[0065] In some embodiments, the system further includes a reader module, the reader module including the imager and an ultraviolet ("UV") lamp. In some embodiments, the processor can control the multichannel pipette to dispense ultraviolet ("UV") glue in the inlet of the PCR cartridge; and control the UV lamp to cure the UV glue in the inlet of the PCR cartridge. In some embodiments, the reader module can include a chip tray, which can receive the PCR cartridge and move the PCR cartridge into the reader module. In some embodiments, the reader module can include a housing. In some embodiments, the UV lamp is located on the housing so that when the PCR cartridge is moved from the chip tray into the reader module, the UV glue is exposed to the UV lamp.

[0066] Further areas of applicability of the present disclosure will become apparent from the detailed description provided hereinafter.It should be understood that the detailed description and specific examples, while indicating various embodiments, are intended for purposes of illustration only and are not necessarily intended to limit the scope of the present disclosure. BRIEF DESCRIPTION OF THE DRAWINGS

[0067] Figure 1 is a perspective view of one embodiment of a system for digital PCR.

[0068] Figure 2 is a perspective view of one embodiment of the system with the door in a second open position.

[0069] Figure 3 is a cross-sectional view taken along cutting plane AA and showing a first layout of the partitions.

[0070] Figure 4 A second layout of the bulkheads is depicted.

[0071] Figure 5 A third layout of the bulkheads is depicted.

[0072] Figure 6 is a schematic diagram of an exemplary consumable.

[0073] Figure 7 is a perspective view of one embodiment of a sample tube system.

[0074] Figure 8 is a top view of one embodiment of a reagent cartridge.

[0075] Fig. 9 is a perspective view of one embodiment of a pipette tip box.

[0076] Fig.10 is a perspective view of one embodiment of a PCR chip as a microwell cartridge and a PCR chip cover.

[0077] Fig.11 is a perspective view of another embodiment of a PCR chip, which is a droplet cartridge.

[0078] Fig.12 is a perspective view of one embodiment of an RNA strip.

[0079] Fig.13 is a perspective view of one embodiment of a droplet generator.

[0080] Fig.14 is a schematic diagram of the controls of one embodiment of the system.

[0081] Fig.15 is a perspective view of one embodiment of a pipette with the drip tray assembly in a stowed position.

[0082] Fig.16 is a side view of one embodiment of a pipette with the drip tray assembly in a stowed position.

[0083] Fig.17 is a perspective view of one embodiment of a pipette with a drip tray assembly in a partially deployed position.

[0084] Fig.18 is a side view of one embodiment of a pipette with the drip tray assembly in a partially deployed position.

[0085] Fig.19 is a perspective view of one embodiment of a pipette in which the drip tray rotates about a vertical displacement member.

[0086] Fig. 20 is a side view of one embodiment of a pipette in which the drip tray rotates about a vertical displacement member.

[0087] Fig.21 is a perspective view of one embodiment of a pipette with the drip tray in an extended position.

[0088] Fig. 22 is a side view of one embodiment of a pipette with the drip tray in an extended position.

[0089] Fig.23 is a flow chart illustrating one embodiment of a method for automated digital PCR.

[0090] Fig.24 is a flow chart illustrating one embodiment of a method for pre-concentrating a sample in a pipette.

[0091] Fig.25 is a graphical depiction of one embodiment of preconcentration in a pipette tip.

[0092] Fig.26It is a graphic depiction of concentration using a magnetic plate.

[0093] Fig. 27 is a flow chart illustrating one embodiment of a method of classifying pixels as belonging to a partition or to the background.

[0094] Fig.28 is a flow chart illustrating one embodiment of a method for performing illumination-independent image normalization.

[0095] Fig.29 is a flow chart illustrating one embodiment of a method for performing illumination-dependent image normalization.

[0096] Fig.30 is a flow chart illustrating one embodiment of a method for single layer detection.

[0097] Fig.31 is a first view of a first window generated by a graphical user interface ("GUI").

[0098] Fig.32 A second window generated by the GUI and configured to facilitate the user creating a batch is depicted.

[0099] Fig.33 is a second view of a first window generated by the GUI.

[0100] Fig.34 is a first view of a third window generated by the GUI.

[0101] Fig.35 is a second view of a third window generated by the GUI.

[0102] Fig.36 is a third view of a third window generated by the GUI.

[0103] Fig.37 is a fourth view of a third window generated by the GUI.

[0104] Fig.38 is a fifth view of a third window generated by the GUI.

[0105] Fig.39 is a sixth view of the third window generated by the GUI.

[0106] Fig.40 It is the fourth window generated by the GUI.

[0107] Fig.41 is a flow chart illustrating one embodiment of a method for performing digital droplet PCR.

[0108] Fig.42is a perspective view of a pipette engaged with a droplet generator. DETAILED DESCRIPTION

[0109] Digital PCR (dPCR) is a method for analyzing nucleic acid molecules. dPCR is a quantitative method in which the target molecules in the sample are separated into many separate reactions and digital analysis is performed to characterize the target molecules. As used herein, each of these separate reactions is described as a partition. As discussed in more detail below, each of these partitions can be formed on a PCR chip, including, for example, in a microwell or as a discrete droplet on a PCR chip. Due to separation, the vast majority of reactions contain one or zero target molecules, which can be detected using different modes. Digital PCR is advantageous because it avoids the potential uncertainty of interpreting fluorescence intensity--any need for time dependence of analog signals--and non-exponential amplification during early cycles.

[0110] However, current platforms and methods for performing digital PCR and / or related analyses may suffer from limitations including: complex setup, low dynamic range, high operator burden, low computational precision due to small number of partitions, lack of automation, lack of integration with sample extraction or purification, low sample utilization (% nucleic acid present in the final reaction compared to input), risk of operator error, throughput, multiplexing capability, slow turnaround time, and other limitations.

[0111] While dPCR has significant benefits, in some embodiments, it may have significant challenges. In many cases, these challenges are closely related to the benefits of digital PCR. For example, because digital PCR is more sensitive than traditional PCR, digital PCR can be used to analyze samples containing smaller amounts of target, such as target nucleic acids including, for example, cell-free DNA. However, these lower concentrations of targets increase the risks associated with contamination and also increase the challenges associated with the concentration of the target and / or the replication of the target.

[0112] Embodiments of systems, devices and methods for providing automated digital PCR are disclosed herein. Such automated digital PCR methods may include sample preparation steps, such as lysing the sample, concentrating the target with, for example, magnetic beads, and / or producing one or more assay mixtures. The automated digital PCR method may further include transferring the prepared sample to a PCR chip, amplifying the target in the PCR chip by thermal cycling, imaging of the PCR chip, and / or analysis of an image of the PCR chip to detect the presence or absence of the target.

[0113] These embodiments include features and / or components for reducing and / or limiting contamination. For example, the system may include a pipette, which may include a drip tray. The drip tray may be expanded to prevent material from falling from the pipette and contaminating the sample. Other features and / or components that may promote reduction and / or limitation of contamination include a graphical user interface ("GUI") that facilitates the setting and / or operation of the assay. The GUI may guide the user to load consumables and / or samples into the system to reduce the risk of contamination. In addition to providing a cover for the sample tube when possible, other features and / or components that may promote reduction and / or limitation of contamination include a baffle layout, internal airflow management. The baffle layout allows the pipette to move in a manner that limits or prevents material from falling from the pipette and contaminating the sample. The module that generates the amplicon, such as the pre-amplification module, is located at the rear of the instrument, and the airflow inside the instrument may be from front to back, so that if contaminants occur, they may be pushed out from other preparation modules. In addition, the sample tube may contain a pierceable membrane or cap to prevent any target molecule from escaping through the air.

[0114] Embodiments disclosed herein may further include features that improve the efficacy of the assay of samples with low concentrations of targets and / or reduce the amount of time required to successfully complete the assay. Such features may include, for example, pre-concentration of the target in the pipette tip. Through this pre-concentration, the efficacy of concentrating the substrate concentration with a magnetic separator can be improved, thereby reducing the time to successfully complete the assay and / or improving the assay efficacy of samples with low concentrations of targets. In some embodiments, additional features that reduce the amount of time to complete the assay include changing the material of one or more consumables to increase thermal conductivity. For example, one or more of the consumables may include plastics doped with heat-conducting materials such as metals to improve the thermal conductivity of the consumables. These doped consumables may have improved thermal conductivity, which can reduce the amount of time required to change the temperature of these consumables and / or change the temperature of the contents of these consumables.

[0115] Some embodiments disclosed herein relate to improved imaging. For example, some embodiments relate to methods of image normalization. This method can utilize an artificial intelligence classifier, which can be a machine learning model for identifying image pixels belonging to a partition and image pixels belonging to a background. The method can further evaluate one or more partition pixels and generate a normalized value, which can then be applied to the pixel value to create a normalized pixel value. These normalized pixel values ​​can increase and / or improve image analysis, and thereby improve the accuracy of digital PCR by mitigating the effects of illumination variations on the PCR chip.

[0116] Some embodiments disclosed herein relate to automatically confirming that sample partitions are correctly generated in a PCR chip. This may include a method for determining whether some or all of the partitions are monolayer partitions. The method may determine whether some or all of the partitions are monolayer partitions through artificial intelligence, and specifically through a machine learning model. Image analysis may then be performed on the monolayer partitions to prevent one or more non-monolayer partitions from causing a bias in the analysis results.

[0117] Combining or sub-combining these various features and embodiments together can create a fully automated system for performing digital PCR. Because of these various features and embodiments, this automated system for performing digital PCR can accurately and quickly perform assays on samples, including samples with small amounts of target.

[0118] Reference now Figure 1 , a perspective view of one embodiment of a system 100 for automated digital PCR is shown. The system 100 can be configured to perform automated sample extraction and digital PCR. The system 100 can be used for any application of digital PCR, including, for example, non-invasive prenatal testing ("NIPT"), fetal fraction ("FF"), oncology screening, genetic screening, carrier screening, including quantification of disease states and / or transplantation panels and / or syndrome panels. In some embodiments, the system can be used to perform digital PCR with, for example, cell-free DNA ("cfDNA"), RNA, cDNA, microRNA, mRNA, mitochondrial DNA, exogenous nucleic acids, and / or genomic DNA.

[0119] In some embodiments, the system 100 can accommodate a sample that can be plasma, and in some embodiments can be 4 mL of plasma. DNA extraction can be performed on the sample, and the DNA extraction can be cfDNA extraction. After the cfDNA extraction has been performed, the workflow scheme performed by the system 100 can vary based on the assay being performed. For example, if cfDNA (e.g., NIPT or cancer or transplant monitoring assay) is being performed, the system 100 can perform DNA quantification, pre-amplification, cfDNA (e.g., NIPT assay preparation, which can include fetal fraction) digital separation, thermal cycling, and imaging. Results can be generated by analyzing images generated during imaging.

[0120] System 100 may include housing 102, which may have a top 104, a bottom 106, a front 108, a rear 110, a first side 112, and a second side 114. Housing 102 may include a variety of shapes and sizes and may be made of a variety of materials. In some embodiments, housing 102 may be made of one or more plastic components, metal components, and / or composite components.

[0121] Housing 102 can define an interior volume in which one or more assays can be performed. In some embodiments, this interior volume can be accessed by door 116, which can be moved from a first position to a second position. In some embodiments, door 116 can enclose the interior volume when it is in the first position, and can provide access to the interior volume when it is in the second position. Figure 1 In the embodiment of the system 100 depicted in , the door 116 in the first closed position is movably connected to the housing 102 via one or more hinges 118 .

[0122] Reference now Figure 2 , shows a perspective view of one embodiment of the system 100, wherein the door 116 is in a second open position, thereby opening the interior volume 120 of the system. Figure 3 As seen in FIG. 1 , a cross-sectional view taken along cutting plane AA and illustrating an interior volume 120 of the system 100 , the interior volume 120 defined by the housing 102 may be divided into a sample preparation module 122 and a reader module 124 .

[0123] The sample preparation module 122 can provide a space for completing sample preparation tasks. The sample preparation module 122 can include, for example, a partition 126 including a plurality of positions 128, each position 128 being configured to receive consumables. In some embodiments, the partition 126 can be removable and / or replaceable. In some embodiments, the partition 126 can be removed and / or replaced to maintain the cleanliness of the partition and / or prevent contamination.

[0124] The consumables that can be stored in position 128 of partition 126 can include, for example, one or more sample tubes, one or more sample tube racks, one or more reagent cartridges, one or more tip boxes, one or more DNA quantitation strips, one or more assay strips, one or more PCR cartridges, one or more PCR cartridge leads, one or more magnetic separation plates, one or more transfer plates, etc. Figure 3 In the illustrated embodiment, each location 128 has its consumables stored.

[0125] In some embodiments, location 128 can be passive in that it only houses consumables, and in some embodiments, location 128 can be active in that it can perform one or more operations on and / or affect consumables. Exemplary active locations 128 can include, for example, pre-amplification thermal cycler 130 (also referred to herein as "pre-amplification thermal cycler 130"), heater / oscillator 132, magnetic separator 134, cooler 136, and RNA heater 138.

[0126] In some embodiments, preamplification thermocycler 130 may be configured to alternately heat and cool the sample in consumables on preamplification thermocycler 130. Preamplification thermocycler 130 may be configured to increase the concentration of the target prior to an amplification step and / or prior to thermal cycling as performed by and / or in reader module 124. In some embodiments, preamplification thermocycler 130 may have particular utility in embodiments where the sample has a low concentration of target.

[0127] The heater / oscillator 132 can accommodate a lysis-binding plate that can include a plurality of holes, and the heater / oscillator 132 can heat and oscillate the sample in the lysis-binding plate. In some embodiments, the lysis-binding plate can include a plastic doped with a metal to increase the thermal conductivity of the lysis-binding plate. In some embodiments, the heating and oscillation of the lysis-binding plate when on the heater / oscillator 132 can promote the lysis of the sample contained in the lysis-binding plate and the binding of the target molecule to the affinity magnetic beads.

[0128] Magnetic separator 134 can accommodate a magnetic separation plate that can include multiple holes. When the target is combined with magnetic beads, magnetic separator 134 can separate the target from other liquids in the hole. Specifically, when the sample combined with the target and magnetic beads is placed in the magnetic separation plate and on the magnetic separator 134, a magnetic field can be generated by the multiple holes of the magnetic separation plate, and the magnetic field can attract magnetic beads. When the magnetic beads are kept in place and in some embodiments, the supernatant can be sucked from one or more holes by the magnetic field against one or more holes and / or a hole, so that the target is separated from the supernatant. This separation can be further improved by one or more washing steps.

[0129] Chiller 136 may facilitate cooling of samples and / or reagents that need to be kept cool while awaiting processing or removal from the instrument.

[0130] The RNA heater 138 may be used to heat samples that may require a different heating regime than that provided by the lysis heater if used simultaneously.

[0131] The reader module 124 may include a thermal cycler and an imager, which may be contained within the reader module housing 140. A PCR chip 142 may be loaded with a sample in the sample preparation module 122, and then the PCR chip 142 may be placed in a chip tray 144. The chip tray 144 may be driven by a motor, which may be controlled to move the chip tray 144 into or out of the reader module 124. Through the chip tray 144, the PCR chip 142 may be moved into the reader module for thermal cycling and / or imaging.

[0132] The internal volume 120 may further include a pipette 150. The pipette 150 may be a multichannel pipette 150 and may include, for example, two channels, three channels, four channels, five channels, six channels, seven channels, eight channels, nine channels, ten channels, 15 channels, 20 channels, or any other or intermediate number of channels. The pipette 150 may be controlled to move above and across the diaphragm 126, for example, on the x-axis or in the x-direction as indicated by arrow 152 and / or on the y-axis or in the y-direction as indicated by arrow 154.

[0133] In some embodiments, the pipette 150 is movably coupled to a gantry 156, which is movably coupled to the housing 102 via tracks 158. The tracks 158 include a first track coupled to the first side 112 of the housing 102 and a second track coupled to the second side 114 of the housing 102. In some embodiments, the pipette 150 can be moved in the x-direction by movement of the gantry 156 along the tracks 158. In some embodiments, such movement of the gantry 156 along the tracks 158 can be caused and / or controlled by an x-axis motor. In some embodiments, the pipette 150 can be moved in the y-direction by movement of the pipette 150 along the gantry 156. In some embodiments, such movement of the pipette 150 along the gantry 156 can be caused and / or controlled by a y-axis motor.

[0134] By combining the track 158 and the gantry 156, the pipette 150 can be moved to a position above each position 128 on the shelf 126 for housing consumables, and thus the consumables and / or the contents of the consumables can be accessed at each of those positions 128. In some embodiments, the pipette 150 can thus be used to aspirate and / or dispense substances from one or several wells, PCR chips, or sample tubes at each position 128.

[0135] The shelves 126 may include different layouts, and in particular may have different arrangements of locations 128 for receiving consumables. Figure 4 , showing a second layout of the partition 126. As can be seen, the partition 126 can be arranged in a manner similar to Figure 3 A similar layout of an embodiment includes a pre-amplification thermal cycler 130 that can hold one or several pre-amplification strips, a heater / oscillator 132 depicted as holding a lysis binding well plate, a magnetic separator 134 depicted as holding a magnetic separation plate, a cooler 136 and an RNA heater 138.

[0136] like Figure 4 As seen in FIG. 1 , the partition 126 further includes one or more sample tube holders 150, which are configured to specifically receive and hold one or more sample tubes. Figure 4 The embodiment of the partition plate 126 shown in FIG. 1 includes four sample tube holders 151 , each of which can hold a plurality of sample tubes, and specifically can each hold eight sample tubes.

[0137] The partition 126 further includes one or more reagent cartridge holders 152. Figure 4 In the illustrated embodiment, the partition 126 includes four cartridge holders 152, each of which can hold a cartridge. In some embodiments, each cartridge in the cartridge can include a plurality of holes that can contain one or more materials, such as one or more reagents for performing an assay.

[0138] The partition 126 includes one or more tip box holders 154. Figure 4 In the illustrated embodiment, the partition 126 includes four tip box holders 154, each of which can hold a tip box. Each tip box can include multiple compartments, and the size and shape of each compartment in the multiple compartments are set to hold a pipette tip. In some embodiments, and during the operation of the system, the pipette 150 can move to a tip box holder in the tip box holder 154, and take out one or several pipette tips from the tip box at the tip box holder 154. Then, these pipette tips can be used by the pipette 150 for one or several pipetting operations, including, for example, aspiration and / or dispensing one or several materials. When the use of the pipette tip is completed, the pipette 150 can return the used pipette tip to the compartment in the tip box. In some embodiments, the compartment in which the used pipette tip is returned is the same compartment from which the pipette tip is obtained.

[0139] The partition 126 includes one or more dosing strip holders 156. Figure 4 In the illustrated embodiment, the spacer 126 includes four quantitation strip holders 156. In some embodiments, each of the quantitation strip holders 156 can hold a quantitation strip. The quantitation strip can include a plurality of holes for DNA quantitation.

[0140] The partition 126 includes one or more test strip holders 158. Figure 4 In the illustrated embodiment, the spacer 126 includes four assay strip holders 158. In some embodiments, each of the assay strip holders 158 can hold an assay strip. An assay strip can contain a plurality of wells for performing one or several assays and / or preparing samples for one or several assays.

[0141] The partition 126 includes one or several PCR cartridge holders 160 and / or one or several PCR cartridge cap holders 162. In some embodiments, the PCR cartridge holder 160 may hold a stack of PCR cartridges, and the PCR cartridge cap holder 162 may hold one or several PCR cartridge caps.

[0142] In some embodiments, the layout of the partitions 126 can improve the efficiency of performing one or several assays with the system 100 and / or can reduce the risk of contamination between samples and / or assays. In some embodiments, such contamination can occur, for example, due to airborne matter such as DNA, dripping of matter such as DNA, difficulty in engaging consumables, gantry accuracy, etc. Such contamination can originate, for example, from the preamplifier thermal cycler, the reader module, or from the sample.

[0143] In some embodiments, the partition layout can mitigate contamination. For example, the locations on the partition 128 can be spaced apart to allow access to consumables at each location. Further, additional space can be provided around consumables and / or locations that may be sources of contamination. Such spacing can mitigate the risk of contamination from airborne matter.

[0144] In some embodiments, for example, the positions 128 on the diaphragm 126 can be arranged so that an assay can be performed on a sample by moving the pipette 150 substantially only in the y-axis. Figure 4 As seen in the embodiment of , the sample tube, reagent cartridge, tip box and DNA quantification strip are arranged generally to form a line extending in the y direction. Therefore, when the assay is performed on the sample, if there is any drop, the drop will fall into the hole associated with the sample.

[0145] In some embodiments, position 128 can be positioned to facilitate engagement of consumables. For example, preamplification thermal cycler 130 can be elevated above the bulkhead. To prevent contamination caused by a user reaching over preamplification thermal cycler 130, preamplification thermal cycler 130 is positioned adjacent to rear portion 110 of housing 102. Further, heater / oscillator 132, magnetic separator 134, and cooler 136 are arranged to be most easily engaged with consumables positioned relatively closest to rear portion 110 of housing 102, and most difficult to engage with consumables positioned relatively closest to front portion 108 of housing 102. For example, at Figure 4 , positioned relatively closest to the rear 110 of the housing 102 is the heater / oscillator 132 , followed by the magnetic separator 134 , and then the cooler 136 .

[0146] The pipette 150 is provided with a starting position close to the intersection of the rear portion 110 and the second side 114. As the pipette 150 moves closer to this initial position, the movement of the pipette 150 is more precise. Therefore, and because the pipette tips have the tightest tolerances, the pipette tips in the tip box 154 are positioned closest to the initial position of the pipette 150.

[0147] Reference now Figure 5 , showing a third layout of the partition 126. The third layout can be configured for digital droplet PCR (DDPCR). As can be seen, the partition 126 can be arranged in a manner similar to Figure 3 and 4 A similar layout of an embodiment includes a pre-amplification thermal cycler 130 that can hold one or several pre-amplification strips, a heater / oscillator 132 depicted as holding a lysis binding well plate, a magnetic separator 134 depicted as holding a magnetic separation plate, a cooler 136 and an RNA heater 138.

[0148] like Figure 5 As seen in FIG. 1 , the partition 126 further includes one or more sample tube holders 150, which are configured to specifically receive and hold one or more sample tubes. Figure 5 The embodiment of the partition plate 126 shown in FIG. 1 includes four sample tube holders 151 , each of which can hold a plurality of sample tubes, and specifically can each hold eight sample tubes.

[0149] The partition 126 further includes one or more reagent cartridge holders 152. Figure 5 In the illustrated embodiment, the partition 126 includes four cartridge holders 152, each of which can hold a cartridge. In some embodiments, each cartridge in the cartridge can include a plurality of holes that can contain one or more materials, such as one or more reagents for performing an assay.

[0150] The partition 126 includes one or more tip box holders 154. Figure 5In the illustrated embodiment, the partition 126 includes four tip box holders 154, each of which can hold a tip box. Each tip box can include multiple compartments, and the size and shape of each compartment in the multiple compartments are set to hold a pipette tip. In some embodiments, and during the operation of the system, the pipette 150 can move to a tip box holder in the tip box holder 154, and take out one or several pipette tips from the tip box at the tip box holder 154. Then, these pipette tips can be used by the pipette 150 for one or several pipetting operations, including, for example, aspiration and / or dispensing one or several materials. When the use of the pipette tip is completed, the pipette 150 can return the used pipette tip to the compartment in the tip box. In some embodiments, the compartment in which the used pipette tip is returned is the same compartment from which the pipette tip is obtained.

[0151] The partition 126 includes one or more dosing strip holders 156. Figure 5 In the illustrated embodiment, the spacer 126 includes four quantitation strip holders 156. In some embodiments, each of the quantitation strip holders 156 can hold a quantitation strip. The quantitation strip can include a plurality of holes for DNA quantitation.

[0152] The partition 126 includes one or more test strip holders 158. Figure 5 In the illustrated embodiment, the spacer 126 includes four assay strip holders 158. In some embodiments, each of the assay strip holders 158 can hold an assay strip. An assay strip can contain a plurality of wells for performing one or several assays and / or preparing samples for one or several assays.

[0153] The partition 126 includes one or several PCR cartridge holders 160 and / or one or several PCR cartridge cap holders 162. In some embodiments, the PCR cartridge holder 160 may hold a stack of PCR cartridges, and the PCR cartridge cap holder 162 may hold one or several PCR cartridge caps.

[0154] The partition 126 may include one or more droplet generators 164. The one or more droplet generators 164 may include one or more droplet generator chips and may be configured to generate droplets for use in DDPCR. In some embodiments, the one or more droplet generators 164 may include one or more droplet generation chips, such as the DG8 sold by Bio-Rad Laboratories, Inc. TM cylinder.

[0155] In some embodiments, the layout of the partitions 126 can improve the efficiency of performing one or several assays with the system 100 and / or can reduce the risk of contamination between samples and / or assays. In some embodiments, such contamination can occur, for example, due to airborne matter such as DNA, dripping of matter such as DNA, difficulty in engaging consumables, gantry accuracy, etc. Such contamination can originate, for example, from the preamplifier thermal cycler, the reader module, or from the sample.

[0156] In some embodiments, the partition layout can mitigate contamination. For example, the locations on the partition 128 can be spaced apart to allow access to consumables at each location. Further, additional space can be provided around consumables and / or locations that may be sources of contamination. Such spacing can mitigate the risk of contamination from airborne matter.

[0157] In some embodiments, for example, the positions 128 on the diaphragm 126 can be arranged so that an assay can be performed on a sample by moving the pipette 150 substantially only in the y-axis. Figure 5 As seen in the embodiment of , the sample tube, reagent cartridge, tip box and DNA quantification strip are arranged generally to form a line extending in the y direction. Therefore, when the assay is performed on the sample, if there is any drop, the drop will fall into the hole associated with the sample.

[0158] In some embodiments, position 128 can be positioned to facilitate engagement of consumables. For example, preamplification thermal cycler 130 can be elevated above the bulkhead. To prevent contamination caused by a user reaching over preamplification thermal cycler 130, preamplification thermal cycler 130 is positioned adjacent to rear portion 110 of housing 102. Further, heater / oscillator 132, magnetic separator 134, and cooler 136 are arranged to be most easily engaged with consumables positioned relatively closest to rear portion 110 of housing 102, and most difficult to engage with consumables positioned relatively closest to front portion 108 of housing 102. For example, at Figure 5 , positioned relatively closest to the rear 110 of the housing 102 is the heater / oscillator 132 , followed by the magnetic separator 134 , and then the cooler 136 .

[0159] The pipette 150 is provided with a starting position close to the intersection of the rear portion 110 and the second side 114. As the pipette 150 moves closer to this initial position, the movement of the pipette 150 is more precise. Therefore, and because the pipette tips have the tightest tolerances, the pipette tips in the tip box 154 are positioned closest to the initial position of the pipette 150.

[0160] refer to Figure 6, a schematic diagram of an exemplary consumable 200 is shown. The consumable 200 can be housed in a position within the partition 126 of the system 100 and can be used to perform an assay. In some embodiments, some or all of the consumables 200 may include one or more holes, the size, shape and spacing of which can be set to be compatible with the pipette 150. In some embodiments, this can include setting the size of the hole to be able to accommodate a pipette tip for aspiration and / or distribution. In some embodiments, this can further include sizing and spacing the holes so that the substance can be aspirated and / or distributed to multiple holes from multiple holes by the multichannel pipette 150 at the same time. Therefore, in some embodiments, the consumable can include 8 rows of holes, the size and spacing of which are set so that the holes in each row of the row can be approached by the pipette 150 at the same time.

[0161] The consumables 200 include a sample tube system 202. The sample tube system 202 can be configured to hold one or more samples. The sample tube system 202 can include a sample tube rack 204 and at least one sample tube 206. In some embodiments, and as Figure 6 As shown, the sample tube rack 204 can hold a plurality of sample tubes 206 , including, for example, eight sample tubes 206 .

[0162] In some embodiments, the sample tube 206 can be configured to hold a sample and can be received within the sample tube rack 204. Figure 7 Shown in.

[0163] Sample tube 206 can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, sample tube 206 can include a polymer that does not affect the sample. Specifically, in some embodiments, sample tube 206 can include an injection molded polymer. The size and shape of sample tube 206 can be set to hold, for example, a sample between about 100 μL and about 2mL, between about 2mL and about 20mL, a sample between about 4mL and about 15mL, a sample between about 5mL and about 8mL, a sample of about 6mL, a sample of about 6.5mL, a sample of about 7mL, a sample of 7.5mL, a sample of 8mL or any other or intermediate volume. As used herein, "approximately" refers to a range extending + / -10% around the identified number and / or the identified range. In some embodiments, sample tube 206 can have a size that allows sample tube 206 to accommodate a 1000 μL pipette tip for aspirating a sample from sample tube 206 and / or distributing the sample to the sample tube.

[0164] In some embodiments, the sample tube 206 may include an identification feature that may identify the sample tube 206. In some embodiments, the identification feature may uniquely identify the sample tube 206. The identification feature may include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature may be located on the sample tube 206 so that it is readable when the sample tube 206 is coupled to the sample rack 204 and / or received in the appropriate position 128 in the bulkhead 126 of the system 100.

[0165] In some embodiments, some or all of the sample tubes 206 may include a magnet located in a portion of the sample tube 206. In some embodiments, the magnet may be located on one side of the sample 206. In some embodiments, the magnet may be positioned in the bulkhead 126 and / or housing such that when the sample tube 206 is received in its position in the bulkhead 126, the magnet is adjacent to one side of the sample tube 206. In some embodiments, the magnet may be used for pipette tip preconcentration, as will be discussed below.

[0166] Consumables 200 include a lysis and combination plate 208. The lysis and combination plate 208 can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, the lysis and combination plate 208 can be configured to hold the sample during the lysis and combination of the sample. In some embodiments, the lysis and combination plate 208 can include one or more reagents for lysis and / or combination, including one or more dry reagents in its holes, and in some embodiments, the reagents for lysis and / or combination can come from a reagent cartridge.

[0167] The lysis and bonding plate 208 may include a polymer that does not affect the sample. In some embodiments, the polymer of the lysis and bonding plate 208 may be doped with a material having a high thermal conductivity, thereby increasing the thermal conductivity of the lysis and bonding plate 208. In some embodiments, for example, the polymer of the lysis and bonding plate 208 may be doped with a metal to increase the thermal conductivity of the lysis and bonding plate 208 and thereby reduce the amount of time required to perform lysis and bonding. Specifically, in some embodiments, the lysis and bonding plate 208 may include an injection molded polymer doped with a metal, such as Makrolon TC621, Makrolon TC 629, Kynar 390, CoolPolyD1202, Coolpoly D5506.

[0168] The lysis-binding plate 208 may include a plurality of wells 210 arranged in 8 rows. In some embodiments, the lysis-binding plate 208 may include 32 wells 210 arranged in 8 rows of four wells 210. In some embodiments, the wells 210 may be sized and shaped to hold, for example, a sample between about 2 mL and about 20 mL, a sample between about 5 mL and about 15 mL, a sample between about 8 mL and about 12 mL, about 8 mL of sample, about 8.5 mL of sample, about 9 mL of sample, about 9.5 mL of sample, about 10 mL of sample, about 10.5 mL of sample, about 11 mL of sample, or any other or intermediate volume of sample. In some embodiments, the wells 210 may have a size such that the lysis-binding plate 208 may receive a 1000 μL pipette tip for aspirating the sample from the wells 210 and / or dispensing the sample to the wells.

[0169] In some embodiments, the cleavage bond plate 208 may include an identification feature that may identify the cleavage bond plate 208. In some embodiments, the identification feature may uniquely identify the cleavage bond plate 208. This identification may include identifying the type of consumable 200, or in other words identifying that the cleavage bond plate 208 is a cleavage bond plate 208, or may uniquely identify a particular cleavage bond plate 208, for example, with an identifier that is specific to the cleavage bond plate 208.

[0170] The identification feature may include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, as well as an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature may be located on the lysing bond plate 208 so as to be readable when the lysing bond plate 208 is received in the appropriate position 128 in the bulkhead 126 of the system 100.

[0171] Consumables 200 include cartridge 212. Cartridge 212 can include various shapes and sizes and can be made of various materials. In certain embodiments, cartridge 212 can be configured to hold substances, such as one or more reagents used during sample preparation. In certain embodiments, sample preparation can include the operation of performing DNA extraction, concentration and purification on the sample. These substances can be dry and aqueous. In certain embodiments, the material in the cartridge can be lyophilized and / or oven dried, and can be sealed in one or more compartments of cartridge 212. In certain embodiments, these reagents can include one or more buffers, primers, probes, detergents, etc.

[0172] In certain embodiments, reagent cartridge 212 may contain and / or contain materials for cell capture and / or processing of sample according to one or more workflows for various applications in one or more compartments. Therefore, reagent cartridge 212 may limit a group of storage volumes distributed on a group of domains, wherein the group of domains may be configured to provide suitable environment and / or volume capacity for the material contents of each domain. The group of storage volumes may directly contain sample processing materials, and / or may alternatively be configured to receive and maintain the position of a single container (e.g., pipe, etc.) containing sample processing materials. The storage volume of each domain may be distributed in an array, or may be otherwise arranged. According to the application (e.g., cold storage, heat transfer, magnetic separation, etc.) used, the storage volume may have a circular cross section, a rectangular cross section, or other forms (e.g., cross section, width, depth, etc.).

[0173] The set of domains may additionally or alternatively be configured to provide modularity, wherein one or more domains may be prepackaged with materials that are stable over a longer shelf life, while other domains may be configured to accommodate materials with a short shelf life (e.g., immediately prior to use). The set of domains may additionally or alternatively be configured to improve the operational efficiency of the devices of the various subsystems described that interact with the materials of the reagent cartridge 212 (e.g., with respect to grouping similar materials, etc.). The set of domains may additionally or alternatively define an area for accommodating and / or processing materials (e.g., nucleic acid materials) extracted from a sample.

[0174] Additionally or alternatively, the domains in the set of domains can be separate (e.g., domains for containing heat are separate from domains intended for other storage temperatures or applications requiring different temperatures), overlapped, or otherwise arranged. The domains in the set of domains can additionally or alternatively be distinguished from each other by morphology (e.g., the length of the storage volume of each domain, the depth of the storage volume for accessing other elements of the baffle or connecting to other elements of the baffle, the width or depth of the domain configured for effective heat transfer, etc.). The internal surface properties of certain domains (e.g., for PCR reactions, for magnetic separation, etc.) can be configured with high surface polish to achieve low binding or retention of biomolecules (e.g., nucleic acids or proteins). Various domains can also be mixed and matched to provide a variety of available assays to customers or other end users.

[0175] A single storage volume in a group of storage volumes of reagent cartridge 212 can further include one or more seals, which are used to isolate the material in reagent cartridge 212, to prevent cross contamination between the material in a single storage volume, to prevent pollutants from entering a single storage volume, and / or to prevent evaporation losses during storage and shipment. Seals can be pierceable seals (e.g., consisting of paper, consisting of metal foil and / or consisting of any other suitable material). However, seals can alternatively be configured to be non-pierceable (e.g., seals can be configured to be peeled off from reagent cartridge 212).

[0176] In a variation, the processing material supported by the domain of the reagent cartridge 212 may include one or more of the following: buffer (e.g., ethanol, initiation buffer, lysis buffer, custom lysis buffer, sample wash buffer, saline containing RNase inhibitors, bead wash buffer, reverse transcription (RT) buffer, etc.), oil (e.g., perfluorinated oil, mineral oil), PCR master mix, beads (e.g., functionalized beads), or any other suitable material for sample processing, target capture, and / or digital analysis. Additionally or alternatively, one or more storage volumes in a set of storage volumes may be empty (e.g., initially empty, empty throughout one or more processes, empty before being filled by an operator, etc.). Different storage areas in the various domains of the reagent cartridge may have an initial reagent volume of from a few microliters (e.g., 5 microliters) to 50 milliliters. In some embodiments, for example, the reagent cartridge 212 may contain a lysis binding buffer, which may include magnetic beads, a washing solution, a protease (e.g., proteinase K) and an elution buffer, mineral oil, a dPCR buffer, etc. In some embodiments, the reagent cartridge may contain a liquid, such as an ultraviolet ("UV") curable glue, for sealing the microfluidic reactor.

[0177] The reagent cartridge 212 may comprise a polymer that does not affect the substances contained within the reagent cartridge 212. In some embodiments, the reagent cartridge 212 may comprise an injection molded polymer.

[0178] Reference now Figure 8 , shows a top view of one embodiment of a reagent cartridge 212. The reagent cartridge 212 may include a plurality of storage compartments 214. These storage compartments 214 may be arranged in eight rows and may therefore include sufficient reagents for sample preparation of eight samples.

[0179] In some embodiments, the reagent cartridge 212 may include 96 compartments 214 arranged in 8 rows of 12 compartments 214. In some embodiments, the size and shape of the compartment 214 may be set to hold, for example, a reagent between about 0.05 mL and about 5 mL, a reagent between about 0.1 mL and about 4 mL, a reagent between about 0.2 mL and about 3 mL, a reagent of about 0.3 mL, a reagent of about 1 mL, a reagent of about 2 mL, or any other or intermediate volume of reagent. In some embodiments, the compartment 214 may include 4 compartments 214 that hold up to 2 mL of reagent in each row of compartments, 2 compartments 214 that hold up to 1 mL of reagent, and 6 compartments 214 that hold up to 0.3 mL of reagent. In some embodiments, the compartment 214 may have a size that allows the reagent cartridge 212 to accommodate, for example, a 50 μL pipette tip, a 1000 μL pipette tip, and / or any other or intermediate pipette tip for aspirating reagents from the compartment 214. In some embodiments, reagent cartridges may contain compartments for holding additional pipette tips and / or other tools (foil piercing tips, cartridge sealing tips, sleeves) required for specific operations during sample processing.

[0180] In some embodiments, the reagent cartridge 212 may include an identification feature that can identify the reagent cartridge 212. In some embodiments, the identification feature can uniquely identify the reagent cartridge 212. Therefore, in some embodiments, each reagent cartridge 212 may include an identifier that is unique to the reagent cartridge 212, unique to the type of the reagent cartridge 212 (e.g., unique to the reagent in the reagent cartridge 212), or unique to the reagent cartridge 212 (e.g., a reagent cartridge 212 of the type of consumables 200 has a unique identifier). The identification feature may include, for example, a computer readable code, such as a bar code, a 2D bar code such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature may be located on the reagent cartridge 212 so that it is readable when the reagent cartridge 212 is received in the appropriate position 128 in the partition 126 of the system 100.

[0181] like Figure 6 As seen in FIG. 1 , the consumables 200 include a pipette tip box 216. The pipette tip box 216 can be configured to receive and / or hold one or more pipette tips. The pipette tip box 216 can include a variety of shapes and sizes and can be made of a variety of materials. The pipette tip box 216 can include a polymer, and in some embodiments, the pipette tip box 216 can include an injection molded polymer doped with a metal.

[0182] The pipette tip box 216 may include a pipette tip tray 218 and a tip box base 220. The pipette tip tray 218 is a generally planar member having a plurality of through holes. In some embodiments, each through hole may be a circular through hole, each through hole forming a circular cylinder for removing material through the tip tray 218. In some embodiments, the size and shape of these through holes may be set so that the pipette tip 222 may be received in the through hole and held in place by the through hole. In some embodiments, the size and shape of the through hole may be set so that the pipette tip may slide in or out of the through hole. In some embodiments, the pipette tip tray 218 may define 96 through holes, each of which may be configured to receive a 50 μL pipette tip, a 1000 μL pipette tip, and / or any other or intermediate pipette tip. In some embodiments, the tip tray 218 may include 8 rows of through holes, each row including 12 through holes.

[0183] The pipette tip box base 220 can include a box-shaped base having an open top and defining an interior volume. The pipette tip tray 218 can be matingly engaged with the pipette tip box base 220 such that the pipette tip tray 218 is coupled to the pipette tip box base 220. In some embodiments, and as Fig. 9 , one or more pipette tips 222 may extend through one or more through holes in the pipette tip tray 218. The pipette tip box base 220 may be sized and shaped to define an internal volume such that the pipette tips are suspended from the pipette tip tray 218 and do not contact each other or a portion of the pipette tip box base 220.

[0184] In some embodiments, the pipette tip box 216 may include an identification feature that can identify the tip box 216. In some embodiments, the identification feature can uniquely identify the pipette tip box 216. The identification feature can include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature can be located on the lyse-bind plate 208 so that it is readable when the pipette tip box 216 is received in the appropriate position 128 in the bulkhead 126 of the system 100.

[0185] The consumable 200 includes a magnetic separation plate 224. The magnetic separation plate 224 can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, the magnetic separation plate 224 can be configured to hold the sample during the magnetic separation of the sample. The magnetic separation plate 224 can include a polymer that does not affect the sample, and in some embodiments, the magnetic separation plate 224 can include an injection molded polymer.

[0186] The magnetic separation plate 224 may include a plurality of separation holes 226 arranged in 8 rows. In some embodiments, the magnetic separation plate 224 may include 96 separation holes 226 arranged in 8 rows of 12 separation holes 226. In some embodiments, the size and shape of the separation hole 226 may be set to hold, for example, a sample of at most about 10 mL, a sample of at most about 8 mL, a sample of at most about 5 mL, a sample of at most about 3 mL, a sample of at most about 2 mL, a sample of about 1.2 mL, or any other or intermediate volume of sample. In some embodiments, the separation hole 226 may have a size that allows the magnetic separation plate 224 to accommodate, for example, a 50 μL pipette tip, a 1000 μL pipette tip, and / or any other or intermediate pipette tip for aspirating reagents from the separation hole 226. In some embodiments, the separation hole 226 and the magnetic separation plate 224 may be compatible with an 8-channel pipette 150, wherein the pipette tip 222 has, for example, a 9 mm spacing.

[0187] In some embodiments, the magnetic separation plate 224 can be placed in the magnetic separator 134. In some embodiments, the magnetic separator 134 can expose the sample in the separation hole 226 of the magnetic separation plate 224 to a magnetic field. The magnetic field can attract the magnetized beads bound to the target in the sample to the wall or bottom of the separation hole 226. In the case where the magnetic beads are fixed by the magnetic field, the supernatant can be aspirated from the separation hole 226. This can be repeated a desired number of times until the desired amount of magnetic beads and targets have been collected in the separation hole 226. In some embodiments, these magnetic beads can be washed once or several times to purify the target bound to the magnetic beads. After completing the washing and purification of the target, the target can be separated from the magnetic beads and collected by elution using a pipette 150.

[0188] In some embodiments, the magnetic separator plate 224 may include an identification feature that can identify the magnetic separator plate 224. In some embodiments, the identification feature can uniquely identify the magnetic separator plate 224. The identification feature can include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature can be located on the magnetic separator plate 224 so that it is readable when the magnetic separator plate 224 is received in the appropriate position 128 in the partition 126 of the system 100.

[0189] The consumable 200 includes an assay strip 228. The assay strip 228 can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, the assay strip can include a polymer that does not affect the sample. Specifically, in some embodiments, the assay strip 228 can include an injection molded polymer. In some embodiments, the polymer of the assay strip 228 can be opaque.

[0190] The assay strip 228 may include a plurality of wells, which may be arranged in a plurality of rows. Figure 6 In an embodiment of the present invention, the assay strip includes 8 rows of wells, each row including two wells. In some embodiments, the wells of the assay strip 228 can hold a volume of dry reagent between about 5 μL and about 10 μL, or any other or intermediate volume of dry reagent. In some embodiments, each well can have a mixing volume between about 10 μL and 30 μL, a mixing volume of about 20 μL, or any other or intermediate mixing volume.

[0191] The size and shape of the hole in the assay strip can be set to receive the pipette tip 222. In some embodiments, this pipette tip 222 can include a 50 μL pipette tip, which can have, for example, a 9 mm spacing. In some embodiments, the hole of the assay strip 228 can have a gap to allow the pipette tip 222 to aspirate the sample from the hole and / or dispense the sample into the hole. In some embodiments, the hole of the assay strip 228 can be sealed. In some embodiments, a penetrable seal that can be a metal and / or metallized seal can be used to seal the hole. In some embodiments, the hole can be sealed with an aluminum seal.

[0192] In some embodiments, assay strip 228 may be configured to and / or may hold one or more dry reagents. In some embodiments, these reagents may be freeze-dried and / or oven-dried. These dry reagents may be specific to the desired assay, or may be commonly available reagents. In some embodiments, these reagents may include a master mix, one or more primers, one or more enzymes, and / or one or more probes.

[0193] In some embodiments, the master mix can be specific to the assay being performed and / or the step being performed. The master mix can include, for example, a pre-amplification master mix, a fetal fraction master mix, a NIPT master mix, and / or any other master mix.

[0194] In some embodiments, the composition and / or concentration of dried reagents in an assay strip may vary based on the PCR chip, such as based on whether the PCR chip includes microwells, or whether the PCR chip is configured for droplets.

[0195] In some embodiments, the assay strip 228 may include an identification feature that can identify the assay strip 228. In some embodiments, the identification feature can uniquely identify the assay strip 228. The identification feature can include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature can be located on the assay strip 228 so that it is readable when the assay strip 228 is received in the appropriate position 128 in the bulkhead 126 of the system 100.

[0196] Consumables 200 include DNA quantitative strips (quantification strip) 230, also referred to herein as DNA quantitative strips (quant strip) 230. DNA quantitative strips 230 can include various shapes and sizes and can be made of various materials. In certain embodiments, DNA quantitative strips 230 can include polymers that do not affect the sample. Specifically, in certain embodiments, DNA quantitative strips 230 can include injection molded polymers. In certain embodiments, the polymers of DNA quantitative strips 230 can be opaque.

[0197] The DNA quantification strip 230 may include a plurality of holes, which may be arranged in a plurality of rows. Figure 6 In the embodiment of the present invention, the assay strip includes 8 rows of holes, each row including one hole. In some embodiments, the holes of the DNA quantitative strip 230 can hold a volume of a dry reagent between about 5 μL and about 10 μL or any other or intermediate volume of a dry reagent. In some embodiments, for example, the filter cake of the dry reagent can occupy a space equivalent to a certain volume, and the volume corresponds to any one of the above-mentioned identification volumes and / or volume ranges. In some embodiments, each hole can have a mixed volume between about 10 μL and 30 μL, a mixed volume of about 20 μL, or any other or intermediate mixed volume.

[0198] The size and shape of the hole in the DNA quantitative strip 230 can be set to receive the pipette tip 222. In some embodiments, this pipette tip 222 can include a 50 μ L pipette tip, which can have, for example, a 9 mm spacing. In some embodiments, the hole of the DNA quantitative strip 230 can have a gap so that the pipette tip 222 aspirates the sample from the hole and / or distributes the sample into the hole. In some embodiments, the hole of the DNA quantitative strip 230 can be sealed. In some embodiments, a penetrable seal that can be a metal and / or metallized seal can be used to seal the hole. In some embodiments, the hole can be sealed with an aluminum seal.

[0199] In some embodiments, DNA quantitative strip 230 can be configured to and / or can hold one or more dry reagents in some embodiments.Alternately, in some embodiments, the reagent for performing DNA quantitative can be located in the reagent cartridge 212.In some embodiments, these reagents can be freeze-dried and / or oven-dried.These dry reagents can be specific to DNA quantitative, and can include, for example, one or more primers and / or one or more probes.In some embodiments, these reagents can include, for example, fluorescent dyes and one or more excipients, such as trehalose.

[0200] In some embodiments, the DNA quantification strip 230 may include an identification feature that can identify the DNA quantification strip 230. In some embodiments, the identification feature can uniquely identify the DNA quantification strip 230. The identification feature may include, for example, a computer-readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature may be located on the DNA quantification strip 230 so that it is readable when the DNA quantification strip 230 is received in the appropriate position 128 in the partition 126 of the system 100.

[0201] The consumables 200 include a pre-amplification strip 232, also referred to herein as a pre-amp strip 232. The pre-amp strip 232 can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, the pre-amp strip 232 can include a polymer that does not affect the sample. Specifically, in some embodiments, the pre-amp strip 232 can include an injection molded polymer. In some embodiments, the polymer of the pre-amp strip 232 can be opaque.

[0202] The preamplification strip 232 may include a plurality of wells, which may be arranged in a plurality of rows. Figure 6In the embodiment of the present invention, the preamplification strip 232 includes 8 rows of holes, each row including one hole. In some embodiments, some or all of the holes in the holes of the preamplification strip 232 may include reagents for preamplification, and in some embodiments, these reagents may be obtained from the reagent cartridge 212. In some embodiments, the holes of the preamplification strip 232 may hold a volume of dry reagents between about 1 μL and about 20 μL, a dry reagent between about 5 μL and about 10 μL, or any other or intermediate volume of dry reagents. In some embodiments, for example, the filter cake of the dry reagent may occupy a space equivalent to a certain volume, which corresponds to any one of the above-mentioned identification volumes and / or volume ranges. In some embodiments, each hole may have a mixed volume between about 1 μL and 40 μL, between about 10 μL and 30 μL, a mixed volume of about 20 μL, or any other or intermediate mixed volume.

[0203] The size and shape of the hole in the preamplification strip 232 can be set to receive the pipette tip 222. In some embodiments, this pipette tip 222 can include a 50 μL pipette tip, a 1000 μL pipette tip, or any other or intermediate volume pipette tip 150, which can have, for example, a 9 mm spacing. In some embodiments, the hole of the preamplification strip 232 can have a gap to allow the pipette tip 222 to aspirate the sample from the hole and / or distribute the sample into the hole. In some embodiments, the hole of the preamplification strip 232 can be sealed. In some embodiments, a penetrable seal that can be a metal and / or metallized seal can be used to seal the hole. In some embodiments, the hole can be sealed with an aluminum seal.

[0204] In some embodiments, preamplification strip 232 can be configured to and / or can hold one or more dry reagents or one or more liquid reagents. In some embodiments, these reagents can be lyophilized and / or oven dried. These dry reagents can be specific for preamplification and can include, for example, one or more primers, one or more enzymes, and / or one or more probes.

[0205] In some embodiments, the preamplification bar 232 may include an identification feature that can identify the preamplification bar 232. In some embodiments, the identification feature can uniquely identify the preamplification bar 232. The identification feature can include, for example, a computer-readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature can be located on the preamplification bar 232 so that it is readable when the preamplification bar 232 is received in the appropriate position 128 in the bulkhead 126 of the system 100.

[0206] Consumables 200 include a PCR chip 234, also referred to herein as a PCR cartridge 234. The PCR chip 234 can be configured to hold multiple partitions for thermal cycling and imaging. These partitions can be in the form of multiple microwells, or in the form of droplets. In some embodiments, these droplets can be water-in-oil droplets. In some embodiments, some or all of the partitions can contain nucleic acids and fluorescent dyes that generate signals in the presence of a target or any nucleic acid.

[0207] The partitions can each have a volume of, for example, less than 1000 picoliters, less than 400 picoliters, less than 300 picoliters, less than 200 picoliters, less than 100 picoliters, less than 50 picoliters, between approximately 10 picoliters and approximately 1000 picoliters, between approximately 125 picoliters and 200 picoliters, a volume of approximately 180 picoliters, or any other or intermediate volume.

[0208] PCR chip 234 can include a variety of shapes and sizes and can be made of a variety of materials. PCR chip 234 can include polymers that allow partition imaging and thermal cycling. In some embodiments, all or part of PCR chip 234 can be optically transparent to facilitate data acquisition. This can include, for example, one or both of the top and bottom of PCR chip 234 being optically transparent. In some embodiments, PCR chip 234 can include one or more flat or smooth surfaces that are configured to be engaged by the suction cup of pipette 150 so that PCR chip 234 can be automatically moved to different locations in system 100.

[0209] In some embodiments, the PCR chip 234 can include a cyclin olefin polymer that can withstand heating up to 120° C. and cycle through temperatures of about 4° C. to about 98° C. In some embodiments, the PCR chip 234 can have a chip configured to enable imaging, including, for example, one or more surfaces through which imaging occurs, which have a SPIA2 finish. In some embodiments, for example, one or both of the top and bottom of the PCR chip 234 can have a SPIA2 finish. In some embodiments, a PCR chip 234 polymer can be selected that has low autofluorescence at the excitation frequency used by the imager.

[0210] PCR chip 234 can include multiple zones for performing different assays. In some embodiments, these zones can include a first zone for performing a first assay, a second zone for performing a second assay, a third zone for performing a third assay, and a fourth zone for performing a fourth assay. In some embodiments, these zones can be arranged in groups so that for a sample, PCR chip 234 includes multiple groups, each group including a first zone, a second zone, a third zone, and / or a fourth zone. In some embodiments, PCR chip 234 can include 8 groups, thereby allowing PCR chip 234 to contain partitions from 8 samples at the same time, and performing thermal cycling and / or imaging to up to 8 samples at the same time.

[0211] The first zone can be configured to receive partitions to perform the first assay. In some embodiments, this first assay may include a NIPT assay. Each first zone in the first zone may have, for example, a determination volume of at most 40 μL, at most 30 μL, at most 20 μL, between about 5 μL and about 20 μL, about 15 μL, or any other or intermediate volume. Each first zone in the first zone on the PCR chip 234 may be configured to receive multiple partitions, and specifically between about 50,000 partitions and about 500,000 partitions, between about 100,000 partitions and about 400,000 partitions, between about 150,000 partitions and about 300,000 partitions, about 200,000 partitions, or any other or intermediate number of partitions. In some embodiments, this may include a first zone that includes a structure such as one or more micropores for receiving a desired number of partitions. In some embodiments, each microwell may comprise a rectangular shape with an open top having a length of 40 microns, a width of 40 microns, and a depth of 60 microns. Such microwells may hold, for example, 96 picoliters.

[0212] The second zone can be configured to receive a partition to perform a second determination. In some embodiments, this second determination can include a fetal fraction determination. Each second zone in the second zone can have, for example, a determination volume of at most 30 μL, at most 20 μL, at most 15 μL, at most 10 μL, between about 5 μL and about 10 μL, about 8 μL, or any other or intermediate volume. Each second zone in the second zone on the PCR chip 234 can be configured to receive multiple partitions, and specifically between about 10,000 partitions and about 500,000 partitions, between about 20,000 partitions and about 250,000 partitions, between about 50,000 partitions and about 150,000 partitions, about 100,000 partitions, or any other or intermediate number of partitions. In some embodiments, this can include a second zone, which includes a structure, such as one or more micropores for receiving a desired number of partitions.

[0213] The third district can be configured to receive partitions to perform the third determination. In certain embodiments, this third determination can include control determination. Each third district in the third district can have, for example, at most 15 μ L, at most 10 μ L, at most 5 μ L, between about 1 μ L and about 5 μ L, about 3 μ L of determination volume or any other or intermediate volume. Each third district in the third district on the PCR chip 234 can be configured to receive multiple partitions, and specifically between about 1,000 partitions and about 100,000 partitions, between about 5,000 partitions and about 50,000 partitions, between about 10,000 partitions and about 30,000 partitions, about 20,000 partitions or any other or intermediate number of partitions. In certain embodiments, this can include the third district, and the third district includes structure, such as one or more micropores for receiving the partition of the desired number.

[0214] The fourth district can be configured to receive partitions to perform the fourth assay. In certain embodiments, this fourth assay can include a DNA quantitative assay. Each fourth district in the fourth district can have, for example, a measurement volume of at most 50 μL, at most 30 μL, at most 25 μL, between about 101 μL and about 30 μL, about 20 μL or any other or intermediate volume. In certain embodiments, each fourth district in the fourth district on the PCR chip 234 can include a single hole, also referred to herein as a quantification well or a quantification well.

[0215] In some embodiments, each first zone in the first zone 252 and each second zone in the second zone 256 is defined by a trench 257. The trench 257 can prevent a sample from one zone 252, 256 from accidentally entering another zone 252, 256. Thus, the trench 257 can divide microwell areas for different samples and / or reaction types. In other embodiments, a portion of a zone is defined by a trench 257, and another portion of the same zone is defined by a trench 257. In other embodiments, one or more zones are defined by a trench 257. In some embodiments, the mouse 257 can have a volume between about 1 μL and about 5 μL, a volume of about 2 μL, or any other or intermediate volume.

[0216] In some embodiments, the size, shape, and / or configuration of the PCR chip 234 can be set to allow samples to be distributed to different features of the PCR chip 234. In some embodiments, for example, the PCR chip 234 can accommodate samples from a 50 μL pipette tip, and specifically a 50 μL filtered pipette tip. In some embodiments, the size, shape, and / or configuration of the PCR chip 234 can be set to accommodate samples from a multi-channel pipette 150, including an 8-channel pipette 150, which can have, for example, a 9 mm pitch.

[0217] The PCR chip 234 may include a microporous cartridge 233 or a droplet cartridge 235. An example of a PCR chip 234 as a microporous cartridge 233 is Fig.10 PCR chip 234 includes a first row 250, which includes a plurality of first regions 252 ( Fig.10 16 first zones are depicted in FIG); a second row 254, the second row including second zones 256 ( Fig.10 8 second zones) and a plurality of quantitative holes 258 ( Fig.10 8 dosing wells are depicted in FIG. 1 ). Each of the first zone 252 and the second zone 256 comprises a plurality of microwells, one microwell per partition. Thus, a zone configured for 100,000 partitions has 100,000 microwells.

[0218] As shown on the microporous cartridge 233, the PCR chip 234 further includes an identification region 260, which may include an identification feature that may identify the PCR chip 234. In some embodiments, the identification feature may uniquely identify the PCR chip 234. The identification feature may include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature may be located on the PCR chip 234 so that it is readable when the PCR chip 234 is received in the PCR cartridge holder 160 on the partition 126 of the system 100.

[0219] Fig.11 A dropper cartridge 235 is depicted. The dropper cartridge 235 includes a first row 250 including a plurality of first zones 252 ( Fig.11 8 first zones are depicted in FIG); a second row 254, the second row including second zones 256 ( Fig.11 8 second zones) and a plurality of quantitative holes 258 ( Fig.11 8 dosing holes are depicted in FIG. 1 ). Each of the first zone 252 and the second zone 256 contains a volume that can be loaded with a plurality of droplets, each droplet forming a partition. Thus, a zone configured for 100,000 partitions can accommodate 100,000 droplets.

[0220] Fig.11 The embodiment includes a third row 253, wherein the third row includes a plurality of third regions 255 ( Fig.118 third zones are depicted in FIG. 1 ). The third zone 255 can be a control zone for performing a control assay. Each of the third zones 255 contains a volume that can be loaded with a plurality of droplets, each droplet forming a partition. Thus, the third zone 255 configured for 100,000 partitions can accommodate 100,000 droplets. The droplets required to fill these reactors can be generated by a variety of methods, such as microfluidic t-junctions to introduce oil and aqueous reagents into the t-junctions, or using multiple picoliter dispensing nozzles or using vibration or agitation induced emulsification of aqueous solutions in oil. Each of the zones 252, 255, 256 includes an inlet, whereby droplets can be loaded into the zones 252, 255, 256 by the pipette 150. Thus, the first zone 252 includes a first inlet 264. In some embodiments, each first zone 252 includes its own unique first inlet 264. Similarly, the second zone 256 includes a second inlet 266. In some embodiments, each second zone 256 includes its own unique second inlet 266. Further, the third zone 255 includes a third inlet 265. In some embodiments, each third zone 255 includes its own unique third inlet 265. Each of these inlets 264, 265, 266 can be sealingly engaged with the pipette tip 222 when the pipette tip 222 is pressed into the inlet 264, 265, 266 with a force between about 1 pound and about 10 pounds, about 5 pounds of force, or any other or intermediate amount of force. In some embodiments, and after one or all of the zones 252, 255, 256 of the dropper cartridge 235 are loaded, the inlets 264, 265, 266 can be sealed. In some embodiments, these inlets can be sealed by an adhesive, which can be, for example, a curable adhesive, such as a UV curable glue.

[0221] After completing the loading and sealing of the droplet cylinder 235, the droplet cylinder 235 and the droplets contained therein can be subjected to thermal cycling. In doing so, the thermal cycler can push against the top surface of the droplet cylinder 235, and in some embodiments, a pressure of at least 3psi can be applied in the entire thermal cycling area. In order to promote thermal cycling, in some embodiments, the top layer of the droplet cylinder 235 can have a heat resistance equivalent to a 1mm thick layer under 1W / mK or greater (e.g., 10W / mK). In some embodiments, the droplet cylinder 235 may include a pressurized plunger 268, which can be engaged by a thermal cycler during thermal cycling to increase the pressure inside the zone 252, 255, 256 by a desired amount, which can be up to 10psi, up to 5psi, up to 3psi, between 1psi and 3psi, about 2psi or any other or intermediate pressure. In some embodiments, the pressurized plunger 268 can be kept compressed during some or all of the thermal cycles.

[0222] As with the microporous cartridge 233, the droplet cartridge 235 further includes an identification region 260, which may include an identification feature that may identify the droplet cartridge 235. In some embodiments, the identification feature may uniquely identify the droplet cartridge 235. The identification feature may include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature may be located on the droplet cartridge 235 so that it is readable when the droplet cartridge 235 is received in the PCR cartridge holder 160 on the partition 126 of the system 100.

[0223] The consumables 200 include a PCR chip cover 236. In embodiments where the PCR chip 234 is a microporous cartridge 233, the PCR chip cover 236 may be configured to sealably couple to the PCR chip 234 to seal the microporous. In some embodiments, for example, the PCR chip cover 236 may be configured to engage with the PCR chip 234 when the PCR chip cover 236 is placed on top of the PCR chip 234. The PCR chip cover 236 may be pressed down on the PCR chip 234, which in some embodiments may cause the PCR chip cover 236 to irreversibly engage with the PCR chip 234. In some embodiments, the PCR chip cover 236 may be applied to the PCR chip, and suction may be applied by the pipette 150. This suction may engage and / or sealably engage the PCR chip cover 236 and the PCR chip 234. In some embodiments, the thermal cycler may compress the PCR chip cover 236 on the PCR chip 234. In some embodiments, this compression may be performed while heating the PCR chip cover 236. In some embodiments, this combination of pressure and heat may sealably couple the PCR chip cover 236 and the PCR chip 234. In some embodiments, and when sealingly applied to the PCR chip 234, the PCR chip cover 236 can seal each of the microwells of the PCR chip 234. In some embodiments, the PCR chip cover can be irreversibly engaged into the PCR chip by pushing a suction cup tool so that a clamp or a living hinge present on one side of the PCR chip cover latches onto the PCR chip cover.

[0224] PCR chip cover 236 can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, the size of PCR chip cover 236 is set to be large enough to seal PCR chip 234, and in some embodiments, PCR chip cover 236 has a thickness that promotes heat transfer and prevents optical interference imaging. In some embodiments, PCR chip cover 236 has a thickness of at most about 3 mm, at most about 2 mm, at most about 1 mm, about 1 mm, or any other or intermediate thickness.

[0225] In some embodiments, the PCR chip cover 236 can include an elastomeric material that is compatible with PCR and creates a thermal interface with a thermal cycler. In some embodiments, the thermal interface has a maximum heat resistance equivalent to a 1 mm thick layer at 1 W / mK. In some embodiments, the elastomeric material of the PCR chip cover 236 can have a thermal conductivity of about 1 W / mK to about 10 W / mK or any other or intermediate thermal conductivity. In some embodiments, the PCR chip cover 236 can be subjected to cycling through temperatures of about 4° C. to about 98° C., and in some embodiments, a PCR chip cover 236 material can be selected that has low autofluorescence at the excitation frequencies used by the imager.

[0226] PCR chip cover 236 Fig.10 . The PCR chip cover 236 includes an identification region 262, which may include an identification feature that can identify the PCR chip cover 236. In some embodiments, the identification feature can uniquely identify the PCR chip cover 236. The identification feature can include, for example, a computer-readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature can be located on the PCR chip cover 236 so that it is readable when the PCR chip cover 236 is received in the PCR cartridge cover holder 162 on the partition 126 of the system 100.

[0227] The consumable 200 includes an RNA strip 270 . Fig.12 The RNA strip 270 shown in the figure can include a variety of shapes and sizes and can be made of a variety of materials. In some embodiments, the determination strip can include a polymer that is compatible with the sample and is heat-conductive. Specifically, in some embodiments, the RNA strip 270 can include an injection molded polymer, which can be a polymer selected for high thermal conductivity, or can be doped with a material to increase the thermal conductivity of the polymer. In some embodiments, for example, the polymer of the RNA strip 270 can be doped with a metal to increase the thermal conductivity of the RNA strip 270. In some embodiments, the polymer of the determination strip 228 can be opaque.

[0228] The RNA strip 270 may include a plurality of holes 272. Fig.12 In the embodiment of the present invention, RNA strip 270 includes 8 rows of holes 272, each row including one hole 272. In some embodiments, the holes 272 of RNA strip 270 can hold a volume of up to 10 mL, up to 5 mL, between about 2 mL and about 6 mL, about 4 mL, or any other or intermediate volume.

[0229] The hole in the RNA strip 270 can be sized and shaped to receive a pipette tip 222. In some embodiments, this pipette tip 222 can include a 50 μL pipette tip, a 1000 μL pipette tip, or any other or intermediate pipette tip 222. In some embodiments, the RNA strip 270 can be compatible with the pipette 150 and / or with the pipette 150 and / or the pipette tip 222, which can have, for example, a 9 mm pitch.

[0230] In some embodiments, the RNA bar 270 may include an identification feature that can identify the RNA bar 270. In some embodiments, the identification feature can uniquely identify the RNA bar 270. The identification feature can include, for example, a computer readable code, such as a barcode, a 2D barcode such as a data matrix code or a QR code, and an alphanumeric code and an electronic identifier such as a radio frequency identifier (RFID) tag, etc. In some embodiments, the identification feature can be located on the RNA bar 270 so that it is readable when the RNA bar 270 is received in the RNA heater 138.

[0231] In some embodiments, the size of the wells in the system 100, and in particular, the volume, can be coordinated to facilitate the transfer of DNA from the assay strip 228 to the PCR chip 234. Specifically, this can include coordinating the volume of the wells of the assay strip 228 with the volume of the PCR chip 234. In some embodiments, for example, such coordination includes making at least one well of the assay strip have the same volume as the total volume of the wells in the PCR chip 234 that will receive the final reaction mixture from one well of the assay strip 228. In some embodiments, such coordination can enable a majority of the DNA to be transferred from the assay strip 228 to the PCR chip 234. In some embodiments, for example, this can include transferring at least 50% of the DNA from the assay strip 228 to the PCR chip 234.

[0232] Reference now Fig.13 , shows a perspective view of one embodiment of a droplet generator 164. The droplet generator 164 can include a variety of shapes and sizes and can be made of a variety of materials. The droplet generator 164 can be configured to generate droplets that can be used to perform DDPCR.

[0233] The droplet generator 164 may include a substrate 280 on which one or more droplet generation units 282 may be positioned. The substrate 280 may include a man-made material, such as a polymer, a ceramic, a composite material, glass, etc. The substrate 280 may include a variety of shapes and sizes, and may be, for example, a rectangular substrate having a length between about 50 mm and about 120 mm, between about 70 mm and about 100 mm, about 88 mm, or any other or intermediate values. In some embodiments, the substrate 280 may have a width between about 10 mm and about 50 mm, a width between about 15 mm and about 40 mm, a width of about 23 mm, or any other or intermediate width.

[0234] The droplet generation unit 282 can be configured to generate droplets for DDPCR, which can be droplets having a diameter between about 10 microns and about 400 microns, a diameter between about 20 microns and about 200 microns, or any other or intermediate diameter. In some embodiments, the droplet generator 164 can have any desired number of droplet generation units 282, including, for example, 1 droplet generation unit 282, 2 droplet generation units 282, 3 droplet generation units 282, 4 droplet generation units 282, 5 droplet generation units 282, 6 droplet generation units 282, 7 droplet generation units 282, 8 droplet generation units 282, 9 droplet generation units 282, 10 droplet generation units 282, 15 droplet generation units 282, 20 droplet generation units 282, or any other or intermediate number of droplet generation units. In some embodiments, the droplet generator 164 may have multiple droplet generation units 282 corresponding to multiple dispensing heads in the pipette 150.

[0235] Each of the droplet generation units may include multiple reservoirs 283. The reservoirs may include a variety of shapes and sizes. Fig.13 In the depicted embodiment, each of the reservoirs 283 comprises a cylindrical reservoir having an outer wall coupled to the substrate 280 at its base, the outer wall and the substrate 280 together defining the interior volume of the reservoir 283. Fig.13 As further depicted in FIG. 2 , some or all of the reservoirs 283 may have an open top so that the pipette 150 may engage the reservoir 283 to pipette liquid into the reservoir 283, draw liquid from the reservoir 28, apply a vacuum to the reservoir 283 to pressurize the reservoir 283, etc.

[0236] The reservoir 283 in the droplet generation unit 282 may include, for example, an oil reservoir 284, a PCR reagent reservoir 286, and a droplet outlet and vacuum port 288, referred to herein as a droplet outlet 288. In some embodiments, the oil reservoir may be configured to receive and hold oil. The oil may include, for example, perfluorinated or silicone oil. In some embodiments, the oil may include perfluorinated oil and / or silicone oil, each of which may be surfactant-containing or surfactant-free. The PCR reagent reservoir 286 may be configured to hold an assay mixture, also referred to herein as a PCR reagent, which may be formed into droplets that may be used for DDPCR by the operation of the droplet generation unit 282.

[0237] The droplet outlet 288 may be a location for outputting droplets generated by the droplet generation unit 282. In some embodiments, the droplet outlet 288 may be sized and / or shaped to engage with a portion of the pipette tube 150 so that droplets may be drawn from the droplet outlet 288 by the pipette 150.

[0238] In some embodiments, and as Fig.13 , some or all of the reservoirs 283 may have a height, which may be the same height, or may be different heights. Thus, in some embodiments, some or all of the reservoirs 283 have the same height. In some embodiments, the height of the reservoir 283 may be, for example, between about 2 mm and about 30 mm, between about 3 mm and about 15 mm, between about 5 mm and about 10 mm, about 7 mm, or any other or intermediate height.

[0239] In some embodiments, the reservoir 283 in the droplet generation unit 282 can be fluidly coupled through one or more channels extending through the substrate 280. In some embodiments, and through these channels, droplets of PCR reagents can be generated, which can be encapsulated in oil.

[0240] Reference now Fig.14, a schematic diagram of the control of one embodiment of the system 100 is shown. As can be seen, the system 100 includes a controller 300. The controller 300 may be configured to receive communications from one or several components of the system 100 and generate control signals that control the operation of those one or several components of the system 100. The controller 300 may include a computing device, and specifically may include and / or may be at least one processor communicatively coupled to a memory 302. The memory 302 may include stored instructions in the form of computer code, which when executed by the processor and / or the controller 300 causes the processor and / or the controller 300 to take one or several actions. The memory 302 may include a main memory and / or a secondary memory. The memory 302 may include, for example, a cache memory, a RAM, a ROM, a PROM, an EPROM, an EEPROM, one or several solid state drives (SSDs), one or several hard drives or hard disk drives, etc. Therefore, in some embodiments, the memory 302 may include volatile and / or non-volatile memory.

[0241] The processor may include one or more microprocessors, such as one or more central processing units (CPUs) and / or one or more graphics processing units (GPUs). The processor may be Advanced MicroDevices, Nvidia etc. are commercially available microprocessors.

[0242] The controller 300 can be in communication with each of the preamplification thermal cycler 130, the oscillator / heater 132, the magnetic separator 134, the cooler 136, the RNA heater 138, and / or the chip tray 144. The controller 300 can receive signals from each of these components and can generate control signals that control the operation of these components. In some embodiments, this can include generating control signals that control, for example, a heater of the preamplification thermal cycler 130, the heater / oscillator 132, the cooler 136, and / or the RNA heater 138. In some embodiments, the control signals generated by the controller 300 can control the opening and / or closing of the chip tray 144. In some embodiments, these control signals generated by the controller 300 can be coordinated so that one or more of these components operate in series, in parallel, and / or partially in parallel.

[0243] Controller 300 is communicatively coupled to display 304. Display 304 may include a screen or monitor. In some embodiments, display 304 may include a touch screen. Display 304 may be configured to provide output to a user, and may be configured to receive input provided from a user and provide those received inputs to controller 300. In some embodiments, display 304 may provide output to a user of system 100, and or several input features, such as one or several keyboards, keypads, mice, microphones, buttons, etc., may provide input from a user to system 100.

[0244] like Fig.14 308. In the embodiment of the present invention, the controller 300 is coupled to the thermal cycler 306 and the imager 308 in communication. The imager 308 and the thermal cycler 306 are components of the reader module 124. In some embodiments, the thermal cycler 306 and the imager 308 can be combined into a single module in the reader module 124. The thermal cycler 306 can be configured to cycle the partitions in the PCR chip 234 and include a heater in some embodiments. In some embodiments, the control signal generated by the controller 300 can control the thermal cycler 306 to control the number of cycles applied to the partitions in the PCR chip 234, control the temperature of the cycles applied to the partitions in the PCR chip 234, control the duration of the cycles applied to the partitions in the PCR chip 234, or control any other aspects of the thermal cycle of the partitions in the PCR chip 234.

[0245] In some embodiments, the controller 300 may further control the thermal cycler 306 to pressurize the PCR chip 234 and / or couple the PCR chip cover 236 to the PCR chip 234. In some embodiments, the controller 300 may further control the thermal cycler 306 to sealably couple the PCR chip cover 236 to the PCR chip 234. In order to control these operations of the thermal cycler 306, the controller 300 may generate a control signal that controls the relative position of the thermal cycler 306 relative to the PCR chip 234 and / or the PCR chip cover 236, and / or controls the operation of the pressurizing plunger 268 of the PCR chip 234.

[0246] In some embodiments, the imager 308 can be configured to generate an image of one or several PCR chips 234 within the reader module 124. In some embodiments, this can include generating a single image that includes the entire PCR chip 234, and in other embodiments, this can include generating multiple images of different regions of the PCR chip 234 that together form an image that includes the entire PCR chip 234. This image can have sufficient resolution so that each partition in the PCR chip 234 can be resolved individually. In some embodiments, this image can have sufficient resolution so that each partition in the PCR chip 234 can be resolved individually by multiple pixels in the image.

[0247] In some embodiments, the controller 300 can analyze the images received from the imager 308. This analysis will be discussed in more detail below, but can include automatic identification of pixels belonging to partitions, image normalization, and automatic identification of single-layer partitions. In some embodiments, this analysis can be performed at least in part by one or more artificial intelligence classifiers and / or machine learning models. In some embodiments, these classifiers and / or models can be trained to generate predictions of outcome probabilities based on inputs received by the classifiers and / or models.

[0248] The imager 308 can be configured to illuminate the PCR chip 234 with excitation energy, and capture one or more images of the PCR chip 234 and / or detect light emitted by the PCR chip 234. In some embodiments, the imager 308 may include one or more excitation sources 310. These excitation sources 310 may include, for example, one or more light bulbs, LEDs, or any other excitation energy sources. In some embodiments, these excitation sources 310 may include one or more filters configured to ensure that the excitation energy irradiating the PCR chip 234 has a desired frequency and / or wavelength. In some embodiments, the imager 308 can be configured to eliminate the PCR chip 234 having six electromagnetic energy frequencies. These six frequencies of electromagnetic energy used for excitation are referred to herein as six channels of excitation energy.

[0249] The imager 308 may include an image capture feature 312, which may include one or more light detection features. In some embodiments, the image capture feature 312 may include one or more filters configured to ensure that the image capture feature 312 captures an image of the PCR chip 234 having a desired light frequency and / or captures a desired frequency of light emitted by the PCR chip 234 and more specifically by the partitions in the PCR chip 234. In some embodiments, the image capture feature 312 may be configured to capture a different set of frequencies for each of the six channels of excitation energy.

[0250] The controller 300 may be communicatively coupled to the pipette 150. Fig.14 As shown, the pipette 150 includes a plurality of components that can be controlled by the controller 300 and / or that are affected by the control of the controller. As previously discussed, the pipette 150 is movably coupled to a gantry 156 that moves on a track 158. The gantry 156 can be moved along the track 158 by an x-motor 314. The x-motor 314 can include any desired motor and / or actuator, including, for example, a stepper motor, a linear actuator, etc. In some embodiments, the x-motor 314 can drive a belt that can be coupled to the gantry, and movement of the belt can cause the gantry 156 to move along the track 158 in a positive x-direction or a negative x-direction.

[0251] The pipette 150 includes a pipette body 316. The pipette body 316 can be moved above and across the partition 126 of the system 100. The pipette body 316 is movably coupled to the gantry 156. The pipette body 316 is movably coupled to the gantry 156 by a y-motor 318. The y-motor 318 can include any desired motor and / or actuator, including, for example, a stepper motor, a linear actuator, etc. In some embodiments, the y-motor 318 can drive a belt that can be coupled to the pipette body 316, and the movement of the belt can move the pipette body 316 along the gantry 156 in a positive y direction or a negative y direction.

[0252] Each of the x-motor 314 and the y-motor 318 is communicatively coupled to the controller. Through this communicatively coupling, the controller 300 can determine, track and / or monitor the position of the pipette 150, and can generate one or more control signals that control the operation of the x-motor 314 and the y-motor 318 to move the pipette 150 to a desired position.

[0253] The pipette body 316 can be movably coupled to the pipette assembly 320. The pipette assembly 320 is movably coupled to the pipette body 316. Specifically, in some embodiments, the pipette assembly 320 can be moved relative to the pipette body 316 on the z-axis. In some embodiments, this can include the pipette assembly 320 moving from a first position at a first vertical distance relative to the partition 126 to a second position at a second vertical position relative to the partition 126. In some embodiments, for example, the first vertical distance from the partition 126 can be greater than the second vertical distance from the partition 126. In some embodiments, when the pipette assembly 320 is above the partition and moves across the partition, the pipette assembly 320 can move to the first position at the first vertical distance from the partition 126, and when the pipette assembly 320 is used and / or is to be used for a pipetting operation, including, for example, aspiration or distribution, the pipette assembly can move to the second position at the second vertical distance from the partition 126.

[0254] In some embodiments, the pipette assembly 320 can be moved relative to the pipette body 316 by a z-motor 322. The z-motor 322 can include any desired motor and / or actuator, including, for example, a stepper motor, a linear actuator, etc. In some embodiments, the z-motor 322 can drive a belt that can be coupled to the pipette assembly 320, and movement of the belt can move the pipette assembly along the pipette body 316 in a positive z-direction or a negative z-direction.

[0255] The pipette assembly 320 includes a sensor 324 or is coupled to the sensor. The sensor 324 can be configured to determine the position of the pipette assembly 320 relative to the partition 126, and specifically, determine the distance from the pipette assembly 320 to the partition 126. The sensor 324 can include any one or several sensors or features, and the sensor or feature is configured to determine the positioning of the pipette assembly 320 relative to the partition 126, and specifically determine the distance from the pipette assembly 320 to the partition 126. In certain embodiments, the sensor 324 can include, for example, a proximity sensor, an ultrasonic sensor, an infrared distance sensor, a laser distance sensor (LIDAR), an LED time-of-flight distance sensor, etc. The sensor 324 can be coupled to the controller 300 in communication, and such information can be provided to the controller 300.

[0256] The z-motor 322 is communicatively coupled to the controller 300. Through this communicatively coupling, the controller 300 can determine, track, and / or monitor the position of the pipette assembly 320 relative to the diaphragm 126 and / or relative to the pipette body 316. In some embodiments, the controller can determine, track, and / or monitor the position of the pipette assembly 320 relative to the diaphragm 126 based on information received from the sensor 324. The controller 300 can generate one or more control signals that control the operation of the z-motor 322 to move the pipette assembly 320 to a desired position and / or in a desired direction.

[0257] The pipette assembly 320 may include a support 326. The support 326 may be a structural member to which a plurality of dispensing heads 328 are coupled. In some embodiments, the pipette 150, and in particular, the pipette assembly may include 1 dispensing head 328, 2 dispensing heads 328, 3 dispensing heads 328, 4 dispensing heads 328, 5 dispensing heads 328, 6 dispensing heads 328, 7 dispensing heads 328, 8 dispensing heads 328, 9 dispensing heads 328, 10 dispensing heads 328, 15 dispensing heads 328, 20 dispensing heads 328, any other or intermediate number of dispensing heads 328.

[0258] Each of the dispensing heads 328 is configured to cooperatively engage with and fluidically couple to the pipette tip 222, and specifically may be coupled to the proximal end 329 of the pipette tip 222, such that the distal end 331 of the pipette tip 222 is below the dispensing head 328 and extends toward the partition 126. Each of the dispensing heads 328 is also fluidly coupled to a pump 332 through a manifold 330. The manifold 330 may be a controllable manifold 330, and specifically may include one or more valves that may be controlled by the controller 300 to selectively couple the dispensing head 328 to the pump 332. In some embodiments, the controller 300 may selectively couple one or more dispensing heads 328 to the pump 332 through the manifold 330.

[0259] The pump 332 may be configured to generate a vacuum to cause aspiration through the pipette tip 222 and / or to generate pressure to cause dispensing through the pipette tip 222. The pump 332 may be communicatively coupled to the controller 300. The controller 300 may receive information from the pump 332 regarding the operation of the pump 332 and / or one or more operating parameters of the pump 332, and the controller 300 may generate one or more control signals that control the operation of the pump 332.

[0260] The pipette assembly 320 may further include or be further coupled to a scanner 334. The scanner 334 may be configured to read the identification features of one or more consumables 200. In some embodiments, the scanner 334 may include, for example, a camera, a barcode reader, an electronic reader such as an RFID tag reader, etc. The scanner 334 may be communicatively coupled to the controller 300 so that the scanner responds to a control signal received from the controller 300 and provides an output to the controller 300. In some embodiments, for example, the controller 300 may enable the scanner 334 to scan the identification features of one or more consumables 200, and the scanner 334 may provide the information to the controller 300. Based on the information received from the scanner 334, the controller 300 may identify the consumables associated with the identification features and / or may identify one or more attributes of the consumables. In some embodiments, and in conjunction with knowing the position of the pipette 150, the controller 300 may determine whether the identified consumables 200 are in the correct position 128 on its partition 126.

[0261] The pipette 150 further includes a drip tray assembly 336. The drip tray assembly 336 can be configured to deploy a drip tray below the pipette 150 and below the distal end 331 of the pipette tip 222 to prevent drops from falling from the pipette tip 222 and / or from the dispensing head 328 and landing on the partition 126 or on or in one of the consumables 200. Thus, the drip tray assembly 336 plays an important role in mitigating the risk of contamination and enabling automated digital PCR. The drip tray can have a removable and replaceable consumable containing a liquid soaked absorbent material.

[0262] The drip tray assembly 336 is movably coupled to the pipette body 316 and can be independently moved relative to both the pipette body 316 and the pipette assembly 320. In some embodiments, the drip tray assembly can be moved by a drip tray z motor 338. The drip tray z motor 338 can include any desired motor and / or actuator, including, for example, a stepper motor, a linear actuator, etc. In some embodiments, the drip tray z motor 338 can drive a belt that can be coupled to the drip tray assembly 336, and movement of the belt can move the drip tray assembly 336 in the positive z direction or the negative z direction.

[0263] The drip tray z-motor 338 is communicatively coupled to the controller 300. Through this communicatively coupling, the controller 300 can determine, track and / or monitor the relative position of the drip tray assembly 336 relative to the pipette body 316 and / or the pipette assembly 320, and specifically monitor whether the drip tray is in the deployed position or in the stowed position. The controller 300 can generate one or more control signals that control the operation of the drip tray z-motor 338 to move the drip tray assembly 336, and specifically the drip tray, to a desired position and / or state.

[0264] The pipette 150 further comprises one or more suction cups 340, such as Fig.14As shown, the suction cup can be coupled to the drip tray assembly 336 and / or can be a part of the drip tray assembly 336. The one or more suction cups 340 can include, for example, 1, 2, 3, 4, 5, 6, 8, 10, 15, 20 or any other or intermediate number of suction cups. In some embodiments, the suction cup 340 can be circular and can have a diameter between 5 mm and 15 mm. The one or more suction cups 340 can be fluidly connected to the pump 332 so that when the one or more suction cups 340 engage with the surface of the object, the pump 332 can generate a vacuum within the suction cup 340. This vacuum can firmly couple the object to the suction cup 340 so that the object can be moved around the partition 126 by the pipette 150. In some embodiments, for example, the pipette 150 can move the PCR chip 234 from the PCR cartridge holder 160 to the chip tray 144, and / or can move the PCR chip cover 236 from the PCR cartridge cover holder 162 to the chip tray 144 to be positioned on top of the PCR chip 234. In some embodiments, and after the reader module 124 completes thermal cycling and imaging, the pipette 150 can remove the PCR chip 234 and / or the PCR chip cover 236 from the chip tray 144 using the suction cup 340. The size of the suction cup and the vacuum applied are selected so that the total vacuum force is greater than the weight of the consumables that must be picked up and transferred from one location to another.

[0265] As previously discussed, the pump 332 is communicatively coupled to the controller 300. Thus, the controller 300 can control the pump 332 to control the vacuum generation in the suction cup 340.

[0266] Reference now Fig.15 , a perspective view of one embodiment of a pipette 150 is shown, wherein the drip tray assembly 336 is in a stowed position. The pipette 150 includes eight pipette tips 222 coupled to a dispensing head 328. The pipette 150 includes a pipette body 316. The pipette body 316 includes a base 400. The base 400 is configured to be movably engaged with the gantry 156, thereby allowing the pipette body 316 and the pipette 150 to be movable relative to the gantry 156, and specifically movable relative to the gantry 156 on the y-axis. The base 400 may include one or more rollers 402, which may ride on the gantry 156 and / or fix the base 400 to the gantry 156.

[0267] Fig.15 The pipette 150 in further includes both a pipette assembly 320 and a drip tray assembly 336 movably coupled to the pipette base 316. As seen, a dispensing head 328 extends distally from the pipette assembly 320, and a pipette tip 222 mated to the dispensing head 328 extends distally under and beyond the dispensing head.

[0268] Arrow 403 indicates the z-axis, wherein the arrow points in the positive z-direction. Thus, with reference to z-axis 403, movement in the opposite direction indicated by the arrow is movement in the negative z-direction, also referred to herein as distal movement.

[0269] Reference now Fig.16 , shows a side view of one embodiment of the pipette 150 with the drip tray assembly 336 in a stowed position.

[0270] Reference now Fig.17 , shows a perspective view of one embodiment of the pipette 150, wherein the drip tray assembly 336 is in a partially deployed position. As can be seen, the drip tray assembly 336 including the drip tray 404 has been advanced distally toward the distal end of the pipette tip 222.

[0271] Reference now Fig.18 , shows a side view of one embodiment of the pipette 150 with the drip tray assembly 336 in a partially deployed position. Fig.17 The drip tray assembly 336 including the drip tray 404 has been advanced distally toward the distal end of the pipette tip 222. Fig.18 As further seen in FIG. 3 , the drip plate assembly 336 has been displaced relative to both the pipette assembly 320 and the pipette body 316 . As further seen, the drip plate assembly 336 includes a suction cup 340 .

[0272] Reference now Fig.19 , shows a perspective view of one embodiment of a pipette 150 in which a drip tray 404 rotates about a vertical displacement member 406. The pipette 150 includes the vertical displacement member 406 as part of the drip tray assembly 336. The drip tray 404 is pivotally coupled to the bottom end of the vertical displacement member 406.

[0273] The drip tray assembly 336 further includes an actuation member 408. The actuation member can be configured to deploy the drip tray 404. In some embodiments, and when the drip tray 404 is deployed or in other words in the deployed position, the drip tray 404 is deployed between the pipette assembly 320 and the diaphragm 126, and specifically between the pipette tip 222 of the dispensing head 328 coupled to the pipette assembly 320 and the diaphragm 126.

[0274] The actuating member 408 has a first end 410 pivotally coupled to the drip tray 404. In some embodiments, the first end 410 of the actuating member 408 is coupled to the drip tray 404 by a pin 412. The actuating member 408 further includes a second end 414 slidably coupled to the drip tray assembly 320. In some embodiments, the actuating member 408 is slidably connected to the drip tray assembly 320 and a feature of the drip tray assembly 336, such as a pin 418, by a slot 416 that extends along a portion of the distance between the second end 414 of the actuating member 408 and the first end 410 of the actuating member 408. As the drip tray assembly 336 is displaced under the pipette assembly 320, the slot 416 of the actuating member 408 slides along the pin 418 until the pin reaches the end of the slot 416 proximate to the second end 414 of the actuating member 408. Once pin 418 has reached the end of slot 416 proximate second end 414 of actuating member 408, drip tray assembly 336 is further displaced downward, in other words, drip tray assembly 336 is further displaced away from door frame 156 causing actuating member 408 to rotate drip tray 404 from a vertical position aligned with vertical displacement member 406 to a horizontal deployed position substantially perpendicular to vertical displacement member 406.

[0275] like Fig.19 As further seen in the drip tray, the drip tray includes a drip tray receiving area 420. When the drip tray 404 is in the deployed position, the drip tray receiving area 420 is located on the top surface of the drip tray 404. The drip tray receiving area 420 can be sized and shaped to receive an absorbent pad. The absorbent pad can be disposable.

[0276] Reference now Fig. 20 , shows a side view of one embodiment of the pipette 150, wherein the drip tray 404 rotates about the vertical displacement member 406. As can be seen, in Fig. 20 4, the drip tray assembly 336 has been advanced distally enough that the pin 418 on the pipette assembly 320 has engaged the end of the slot 416 of the actuation member 408 proximal to the second end 414 and caused the drip tray 404 to automatically rotate about its pivotal connection with the vertical displacement member 406. Thus, in some embodiments, through the interaction of the actuation member 408, the drip tray 404 can be automatically deployed between the diaphragm 126 and at least one pipette tip 222 of one of the dispensing heads 328 coupled to the pipette assembly 320.

[0277] Reference now Fig.21 , shows a perspective view of one embodiment of the pipette 150, wherein the drip tray 404 is in the deployed position. As can be seen, in this position, the drip tray assembly 336 is fully displaced distally so that the drip tray 404 is in the deployed configuration and is positioned distally below the distal end 331 of the pipette tip 222.

[0278] Reference now Fig. 22 , shows a side view of one embodiment of the pipette 150, wherein the drip tray 404 is in the deployed position. As can be seen, the drip tray 404 in the deployed position extends generally perpendicular to the vertical displacement member 406, or in other words, rotated to be generally perpendicular to the z-axis. In this position, and as shown Fig. 22 As seen in FIG. 4 , the drip tray 404 is positioned distally below the distal end 331 of the pipette tip 222, and any drips from the pipette tip 222 will be caught by the drip tray 404. Fig. 22 As further seen in FIG. 4 , suction cup 340 is coupled to vertical displacement member 406. Specifically, suction cup 340 is coupled to vertical displacement member 406 such that when drip tray 404 is deployed, suction cup 340 is also deployed. In the deployed position, and as shown in FIG. Fig. 22 As can be seen, the suction cup extends distally beyond the drip tray 404. Due to this distal extension, the suction cup 340 can be engaged with an object such as a PCR chip 234 and / or a PCR chip cover 236. When engaged with an object such as a PCR chip 234 and / or a PCR chip cover 236, the controller 300 can control the pump 332 to generate a vacuum, thereby coupling the object such as a PCR chip 234 and / or a PCR chip cover 236 to the suction cup 340 to allow the object such as a PCR chip 234 and / or a PCR chip cover 236 to be moved to different positions on the diaphragm 126 by the pipette 150.

[0279] In some embodiments, drip tray 404 can be moved back to the undeployed configuration by moving drip tray assembly 336 in the positive z-direction, whereby drip tray 404 is moved from Fig. 22 The horizontal position depicted in the figure moves to Fig.16 In some embodiments, the drip tray 404 can be biased to the non-deployed position by, for example, a spring.

[0280] In some embodiments, the pipette 150 can be used to perform automated digital PCR. This can include receiving the sample tube 206 in a sample tube holder 151 in the partition 126 of the automated digital PCR system 100. The pipette tip 222 coupled to the pipette 150 can be moved distally toward the partition 126 to insert the pipette tip 222 into the sample tube 206. The operation of the pump 332 can then be controlled by the controller 300 to draw a portion of the sample from the sample tube 206 into the pipette tip 222 coupled to the pipette 150. The pipette tip 222 can then be moved away from the partition 126, thereby retracting the pipette tip 222 from the sample tube 206. The drip tray 404 can be automatically deployed between the pipette tip 222 and the partition 126, as shown in FIG. Figure 13-20 shown.

[0281] The pipette 150 and the pipette body 316 can then be moved over and across the diaphragm 126 until they are positioned over an object, such as a PCR chip 234 or a PCR chip cover 236. The drip tray assembly 336 can be moved toward the diaphragm 126 until the suction cup 340 engages with the object, such as a PCR chip 234 or a PCR chip cover 236. The controller 300 can control the pump 332 to generate a vacuum within the suction cup, thereby coupling the object to the suction cup 340. While maintaining the coupling, in some embodiments, while maintaining the vacuum, the drip tray assembly 336 moves away from the diaphragm 126, and the pipette 150 and / or the pipette body 316 moves over and across the diaphragm 126 to another position, for example, to a position over the chip tray 144. The drip tray assembly 336 may be moved toward the shelf 126 to position the object in the chip tray 144 , at which time the controller 300 may control the pump 332 to release the object from the suction cup 340 .

[0282] Reference now Fig.23 , a flow chart showing one embodiment of a method 500 for automated digital PCR is shown. The method 500 may be performed by all or part of the system 100. In some embodiments, the method 500 may be performed according to instructions provided by the GUI through the display 304, as controlled by the controller 300. The method 500 may include determining, generating and / or collecting data, values ​​and / or images. In some embodiments, some or all of these data, values ​​and / or images may be stored in one or more databases in the memory 302.

[0283] Method 500 may include a number of core steps that will be explained in more detail below. These include: performing pipetting operations with the multichannel pipette to transfer a portion of the sample from the sample tube into a PCR cartridge; thermal cycling the sample in the PCR cartridge with the heater; and imaging the sample in the PCR cartridge with the imager. In some embodiments, performing these pipetting operations may include moving the drip tray 404 from a non-deployed position to a deployed position to prevent droplets from the pipette 150 from falling onto the partition 126 or onto the consumables 200. In some embodiments, the drip tray 404 may be moved to the deployed position each time the pipette 150 is moved over and across the partition 126. In some embodiments, the drip tray 404 is held in the deployed position until the pipette is in a position to aspirate or dispense.

[0284] The method 500 begins at block 502, where a user places one or more samples in a holder on the bulkhead 126 of the system 100. As used herein, "sample" and "plasma" are equivalent. In some embodiments, this may include placing one or more sample tubes 206 containing the sample in a sample tube holder 151 on the bulkhead 126 of the system 100.

[0285] In some embodiments, the sample tube 206 is part of the sample tube system 202. Specifically, in some embodiments, the sample tube system 202 can include a sample tube rack 204 in the sample tube 206. In some embodiments, the sample tube 206 can be received in the sample tube rack 204, and the sample tube system 202 can be received in the sample tube holder 151.

[0286] In some embodiments, and as part of the steps of box 502, the system 100 can confirm that the sample is received in a holder on the bulkhead 126 of the system 100. In some embodiments, this can include confirming that the one or more sample tubes 206 are received in the sample tube holder 151 in the bulkhead 126. In some embodiments, this confirmation can include scanning and identifying features on the sample tube 206 received in the sample tube holder 151, and comparing the identification features and / or information encoded in the identification features with information identifying the sample tube 206 expected to be received in the sample tube holder 151. If the information from the identification features and / or the identification features match the information of the expected sample tube 206, then the sample tube holder 151 that receives the expected sample tube 206 can be confirmed.

[0287] At block 504, the sample is lysed. In some embodiments, this may include picking up a pipette tip 222 from the tip box 216 using the pipette 150. The pipette 150 may aspirate plasma from the sample tube 206 using the pipette tip 222 and dispense the aspirated sample into the lysis / binding plate 208. In some embodiments, and after the pipette 150 has aspirated plasma, the drip tray 404 may be placed in an extended position to catch any droplets that fall from the pipette 150. In some embodiments, the pipette 150 may aspirate 1 mL of plasma and transfer the plasma from the sample tube to one of the wells in the lysis / binding plate 208. This transfer may be repeated, transferring plasma from one of the sample tubes 206 to the wells in the lysis / binding plate 208 until, for example, 4 mL of plasma has been transferred to one of the wells in the lysis / binding plate 208.

[0288] The pipette 150 can be used to transfer one or more reagents, such as an enzyme that causes lysis, such as a protease, such as proteinase K, from the reagent cartridge 212 to the wells in the lysis / binding plate 208 containing the transferred sample. In some embodiments, the pipette 150 can be used to mix one or more reagents with the plasma in the wells of the lysis / binding plate 208 by repeatedly aspirating and dispensing the solution from the wells. The sample and reagents in the wells of the lysis / binding plate 208 can be incubated and / or shaken for a period of time. In some embodiments, this can include incubating the sample and reagents at a temperature of 37° C. in the wells of the lysis / binding plate 208 for between 10 minutes and 20 minutes, and in some embodiments for about 15 minutes. In some embodiments, the lysis / binding plate 208 can be shaken while incubating, for example, at about 1500 RPM.

[0289] At frame 506, the lysed sample can be combined with magnetic beads. In some embodiments, this can include transferring the binding solution from the reagent cartridge 212 to the hole of the lysis / binding plate 208 with a pipette 150. The binding agent that can include magnetic beads for binding to nucleic acids can be mixed with the sampling reagent in the hole of the lysis / binding plate 208. In some embodiments, the sample, reagent and binding solution can be incubated and / or shaken for a period of time. In some embodiments, this can include incubating the sample, reagent and binding solution at a temperature of 37° C. in the hole of the lysis binding plate 208 for 10 to 20 minutes, and in some embodiments for about 15 minutes. In some embodiments, the lysis / binding plate 208 can be shaken while incubating at, for example, about 1500RPM. In some embodiments, the steps of frames 504 and 506 can be performed separately, and in some embodiments, the steps of frames 504 and 506 can be combined so that both reagents and binding solutions are added to the hole containing plasma and then incubated together.

[0290] At step 508, the magnetic beads bound to the nucleic acid are separated from the supernatant. In some embodiments, this may include performing a pre-concentration method in the pipette tip 222, as will be discussed in more detail below, and / or may include separating the magnetic beads from the supernatant by the magnetic separator 134. In some embodiments, the pre-concentration method may include aspirating 1 mL of a solution including sampled beads, and increasing the concentration of magnetic beads in the solution by 10x while in the pipette tip 222. In some embodiments, separating the magnetic beads from the supernatant by the magnetic separator 134 may include aspirating the lysed sample including the magnetic beads from the wells of the lysis / binding plate 208 with a pipette 150, and transferring it to the wells of a magnetic separation plate 224 on the magnetic separator 134. In some embodiments, the solution including the magnetic beads and the bound nucleic acids dispensed to the wells of the magnetic separation plate 224 has been pre-concentrated in the pipette tip 222.

[0291] When in the hole of magnetic separation plate 224, magnetic field can be applied to the solution comprising magnetic beads to promote the further concentration of magnetic beads.When magnetic beads are held in place by the applied magnetic field, supernatant can be sucked from the hole of magnetic separation plate 224.After having sucked enough supernatant from the hole of magnetic separation plate 224, one or several washings can be carried out to further purify the nucleic acid combined with magnetic beads.These washings can include washing solution mixed with magnetic beads, magnetic field is applied to the combination of washing solution and magnetic beads, and when magnetic beads are held in place by magnetic field, supernatant is sucked from the hole of magnetic separation plate 224.Supernatant can be discarded in the hole of reagent cartridge 212 by pipette 150.These washings can be carried out repeatedly to realize the desired purity of nucleic acid in the hole of magnetic separation plate 224.

[0292] At block 510, the nucleic acids are eluted from the magnetic beads. In some embodiments, this may include aspirating an elution buffer from the wells of the reagent cartridge 212 and transferring the elution buffer to the wells of the magnetic separation plate 226. The elution buffer may be allowed to sit, mixing with the magnetic beads for a period of time, during which the nucleic acids are separated from the magnetic beads.

[0293] At block 512, the eluted sample may be transferred to one or more wells of an assay strip 228 to produce one or more assay mixtures 512. In some embodiments, this may include transferring portions of the eluted sample to different wells of an assay strip 228, each of which may correspond to an assay and may contain one or more reagents and / or master mixes for the assay. In some embodiments, for example, this may include a first well for a first assay such as a NIPT assay and a second well for a second assay such as a FF assay.

[0294] In some embodiments, additional DNA or nucleic acid quantitative steps may be performed at any appropriate time, such as after eluting the sample and before transferring the eluted sample to one or several holes of the assay strip 228, or any other time that may be appropriate. This quantitative step is quantitative to the nucleic acid in the sample and / or the eluted sample, and in some embodiments, the DNA in the sample and / or the eluted sample is quantitative. The quantitative step may include aspirating or distributing the quantitative reagent, for example, from the reagent cartridge 212 to the hole of the quantitative strip 230 with a pipette 150. In some embodiments, the quantitative reagent may already be in the hole of the quantitative strip 230. A portion of the sample or the eluted sample, such as 2 μL of the eluted sample, may be aspirated and may be distributed to the hole of the quantitative strip. The quantitative reagent and a portion of the sample and / or the eluted sample may be mixed by the pipette 150, and then may be transferred to a quantitative hole in the quantitative hole 258 of the PCR chip 234 by the pipette 150. The PCR chip is then imaged by an imager to detect the amount of nucleic acid, such as by imaging the fluorescence amount. In some embodiments, pre-stored calibration values ​​can be used to quantify nucleic acids in quantification wells 258. Quantification information can be used to determine the amount of sample required to perform certain steps of an assay or to understand results generated by a certain volume of sample and / or eluted sample.

[0295] In some embodiments, and before the eluted sample is transferred to the assay strip 228, a preamplification protocol can be performed to increase the amount of nucleic acid in the sample. This can include transferring the buffer used for preamplification from the reagent cartridge 212 to the preamplification strip 232 with the pipette 150. Strip 232. A certain amount of the eluted sample can be aspirated from the wells of the magnetic separation plate 226 by the pipette 150 and can be transferred to the wells of the preamplification strip 232 containing the preamplification PCR buffer. The preamplification PCR buffer can be mixed with the eluted sample in the wells of the preamplification strip 232 by repeated aspiration and dispensing by the pipette 150.

[0296] An oil layer, such as a mineral oil layer, may be created above the mixture of preamplification PCR buffer and eluted sample in the wells of the preamplification strip 232. The layer may be created by transferring the oil from the reagent cartridge 212 into the wells of the preamplification strip using a pipette 150. After this oil layer has been created, the mixture of sample and preamplification solution may be thermally cycled by the preamplification thermal cycler 130.

[0297] At block 514, the assay mixture is transferred from the assay strip 238 to the PCR chip 234. In some embodiments, this transfer can be performed by a pipette 150. In embodiments where the PCR chip includes a plurality of microwells, transferring the assay mixture to the PCR chip 234 can include aspirating a portion of the assay mixture from the assay strip 238 and dispensing the portion of the assay mixture into a plurality of microwells in one of the zones 252, 255, 256 of the PCR chip 234. This can be repeated until all of the assay mixture or assay mixtures have been transferred to the microwells on the PCR chip 234.

[0298] Alternatively, the PCR chip 234 is configured for droplets, and transferring the assay mixture to the PCR chip 234 may include aspirating a portion of the assay mixture from the assay strip 238 with a pipette, and dispensing the portion of the assay mixture into a microfluidic device configured to generate droplets, which are then loaded into the PCR chip 234. This may be repeated until all of the assay mixture or the assay mixtures have been transferred to the zones 252, 255, 256 of the PCR chip 234.

[0299] At block 516, and in the case where the PCR chip 234 includes a plurality of microwells, the PCR chip cover 236 is removed with the pipette 150 and secured to the PCR chip 234. In some embodiments, the PCR chip cover 236 can be removed from the PCR chip cover holder 162 with the suction cup 340 of the pipette 150 and can be placed on the PCR chip 234 in the chip tray 144. In some embodiments, with sufficient force, the pipette can press the PCR chip cover 236 onto the PCR chip 234 to couple the PCR chip cover 236 to the PCR chip 234. In some embodiments, the PCR chip cover 236 can be sealed to the PCR chip 234, and the microwells on the PCR chip 234 can be sealed by applying heat to the PCR chip cover 236 and the PCR chip 234 by the thermal cycler 306. In some embodiments, sealing the PCR chip cover 236 to the PCR chip 234 can include sliding the chip tray 144 into the reader module 124, and then contacting the thermal cycler 306 with the PCR chip cover 236.

[0300] At box 518, the PCR chip 234 is moved to the thermal cycler 306, and the PCR chip 234 and the partitions on the PCR chip 234 are thermally cycled. At box 520, the PCR chip 234, and specifically the partitions of the PCR chip, are imaged by the imager 308. In some embodiments, this can include irradiating the PCR chip 234 with excitation energy from the excitation source 310, and capturing one or several images of the PCR chip 234 with the image capture feature 312, in some embodiments, the image capture feature can include a camera, and the PCR chip 234 can be imaged with six channels of excitation energy and corresponding images. In some embodiments, each PCR chip 234 can generate multiple images, including, for example, between 5 and 250 images, between 20 and 100 images, about 50 images, or any other or intermediate number of images.

[0301] Reference now Fig.24 , a flow chart illustrating one embodiment of a method 600 for pre-concentrating a sample in a pipette tip 222 is shown. The method 600 may be performed by all or part of the system 100, including the pipette 150 and the pipette tip 222. In some embodiments, the method 600 may be performed as part of the steps of the block 508 method 500.

[0302] Method 600 can be performed iteratively to pre-concentrate the sample before further separation, washing, and purification with magnetic separation plate 224 and magnetic plate 134. In some embodiments, method 600 includes: aspirating a first sample containing a plurality of nucleic acids bound to magnetic beads into a pipette tip of a pipette; positioning the pipette tip of the pipette adjacent to a magnet, and thereby attracting the magnetic beads to the magnet; and concentrating the magnetic beads of the first sample in the pipette tip by dispensing a portion of the first sample when the pipette tip is adjacent to the magnet. By positioning the pipette tip adjacent to the magnet, the magnetic beads are attracted to the magnet to retain the magnetic beads in the undispensed portion of the first sample.

[0303] The remainder of the sample is dispensed into the wells in the magnetic separation plate 224, and the preconcentration is repeated for a second sample, a third sample, and so on, until a desired amount of the preconcentrated sample is collected in the wells of the magnetic separation plate 224. This may include, for example, concentrating magnetic beads for the second sample in a pipette tip by dispensing a portion of the second sample while the pipette tip is adjacent to a magnet, and dispensing the remainder of the second sample into the wells in the magnetic separation plate 224. As with the first sample, attracting the magnetic beads to the magnet retains the magnetic beads in the undispensed portion of the second sample.

[0304] After a sufficient amount of the pre-concentrated sample is collected in the wells of the magnet plate, the pre-concentrated sample can be exposed to a magnetic field that fixes the position of the magnetic beads when the supernatant is aspirated from the wells. Thus, in some embodiments, this can include aspirating the remaining portion of the first sample and the second sample from the wells in the magnetic separation plate 224, with the magnetic field holding the magnetic beads within the wells.

[0305] The method 600 begins at block 602, where a fluid containing plasma and magnetic beads is aspirated by the pipette 150 into the pipette tip 222. In some embodiments, the fluid containing plasma and magnetic beads contains nucleic acids bound to the magnetic beads, and specifically may contain a plurality of nucleic acids bound to the magnetic beads.

[0306] At frame 604, the drip tray 404 is moved to a second deployed position. At frame 606, the pipette 150 is moved to a position above a container containing a magnet and / or adjacent to a magnet. In some embodiments, the magnet can be a magnetic bar. In some embodiments, the container can contain a sample tube 206. In some embodiments, the magnet can be a part of the sample tube 206, or can be located in a partition 126 adjacent to the sample tube 206. In some embodiments, for example, the magnet can include a magnetic bar, which can be located, for example, in one side of the sample tube 206.

[0307] At block 608, the drip tray 404 is moved to the first undeployed position. At block 610, the pipette tip 222 is then positioned so that a portion of the pipette tip is adjacent to the magnet. In some embodiments, this may include shifting the pipette tip 222 in the negative z-direction toward the diaphragm 126 until the distal end 331 of the pipette tip 222 extends into the container and below the distal side of the magnet.

[0308] Fig.23 (a) shows such positioning of the pipette tip relative to the container, and specifically relative to the sample tube 206. As can be seen, the distal end 331 of the pipette tip 222, which includes a proximal end 329 and a distal end 331 and contains a sample 650, is advanced distally into the sample tube 206 and is positioned adjacent to a magnet 652, which may be located in a side 654 of the sample tube 206. The pipette tip 222 is positioned adjacent to the magnet 652 such that the magnet is located intermediate the proximal end 329 and the distal end 331 of the pipette tip 222.

[0309] At block 612, a majority of the fluid, and more specifically, the supernatant, is dispensed from the pipette tip 222. In some embodiments, this may include dispensing between about 50% and about 95% of the fluid and / or sample aspirated in block 602 into the pipette tip 222, and in some embodiments, may include dispensing about 90% of the fluid and / or sample aspirated in block 602 into the pipette tip 222.

[0310] like Fig.23 (b), the pipette tip 222 is positioned adjacent to the magnet 652 such that the distal end 331 of the pipette tip 222 extends below the magnet 652 and into the sample tube 206, and such that the sample 650 extends proximally above the magnet 652. As further seen, due to the magnetic field generated by the magnet 652, the magnetic beads 656 are attracted to the magnet 652 such that the position of the magnetic beads 656 is maintained while a portion of the fluid aspirated in the frame 602, i.e., a portion of the supernatant 658, is dispensed from the pipette tip 222 and into the container, and specifically into the sample tube 206.

[0311] As discussed above, a first portion 658(a), also referred to herein as the dispensed portion 658(a) of the supernatant, is dispensed into a container, and specifically into the sample tube 206, and a second portion 658(b), also referred to herein as the retained portion 658(b) of the supernatant, is retained in the pipette tip 222. In some embodiments, and after the dispensing of the first portion 658(a) of the supernatant is complete, the second portion 658(b) of the supernatant extends proximally over the magnet 652.

[0312] At block 614, the remaining portion of the fluid in the pipette tip 222, i.e., the second portion 658(b), is transferred by the pipette 150 to the magnetic separation plate 226 for further concentration. Fig.26 , this can include dispensing the second portion 658(b) into a well 660 in the plurality of wells of the magnetic separation plate 224. The well 660 of the magnetic separation plate 224 can be adjacent to a magnet 662 such that the magnetic beads 656 are concentrated adjacent to the magnet 662 and held in place by the magnet 662. While the magnetic beads 656 are held in place by the magnet 662, supernatant can be aspirated from the well 660 of the magnetic separation plate 226, one or several washes can be performed, and / or nucleic acids can be eluted from the magnetic beads 656.

[0313] Reference now Fig. 27 , a flow chart is shown, which illustrates an embodiment of a method 700 for classifying pixels as belonging to a partition or background. The method 700 may be performed by all or part of the system 100. The method 700 may be used as Fig.23 The method 700 may include determining, generating and / or collecting data, values ​​and / or images. In some embodiments, some or all of these data, values ​​and / or images may be stored in one or more databases in the memory 302.

[0314] Method 700 begins at block 702, where an area to be imaged is irradiated. In some embodiments, the area to be imaged is a PCR chip 234, and specifically, the entirety of the PCR chip 234. In some embodiments, the area to be imaged is irradiated by one or several excitation sources 310 of an imager 308. In some embodiments, the irradiation of the area to be imaged can be done at one or several frequencies, and in some embodiments, can be performed with some or all of the channels of excitation energy.

[0315] At block 704, at least one image of the irradiated area is generated. The image of the irradiated area may be an image of the PCR chip 234, and specifically may be an image of the entire image capture feature 312. In some embodiments, at least one captured image is generated at one or several frequencies, and in some embodiments, may be captured with some or all of the channels of excitation energy.

[0316] At box 706, an artificial intelligence model can be used to predict the probability that each pixel in at least one image belongs to a partition, and the artificial intelligence model can be, for example, a machine learning model, and more specifically a machine learning classifier. In some embodiments, this can include identifying each pixel in the image, the pixel value of the pixel, and / or the location of the pixel. One or more of these pixel attributes, and in some embodiments, the attributes of one or more neighboring pixels, can be provided as features for the model to predict the probability. Therefore, in some embodiments, one or more of these pixel attributes, and in some embodiments, the attributes of one or more neighboring pixels can be provided as input to the model, and the model can predict the probability that the pixel belongs to a partition based on the input.

[0317] As shown in frame 708, for each pixel, the probability that the pixel belongs to a partition is compared with a threshold value. Based on this comparison, each pixel is determined to belong to a background or potential partition. The location of the pixel identified as belonging to the potential partition is identified, and the candidate partition is identified, as shown in frame 710. In some embodiments, each candidate partition comprises a plurality of adjacent potential partition pixels, which in some embodiments may be surrounded by background pixels. After each adjacent potential partition pixel is identified as belonging to a candidate partition, the size of each candidate partition is determined. In some embodiments, the size of each candidate partition pixel may be determined based on the size of the candidate partition and / or based on the number of pixels in the candidate partition.

[0318] As shown in block 712, each candidate partition grouping is compared to a series of thresholds to determine whether the candidate partition grouping represents a partition. In some embodiments, these thresholds may include a maximum size threshold and a minimum size threshold. At decision step 714, it is determined whether the candidate partition grouping is within a threshold range, or in other words, is greater than the minimum threshold and less than the maximum threshold. In some embodiments, when the size of the candidate partition grouping is greater than the minimum size threshold and less than the maximum size threshold, the candidate partition grouping is identified as representing a partition.

[0319] If it is determined that the candidate partition group is not within the threshold range, the method 700 proceeds to block 716 and the candidate partition group is discarded. Alternatively, if it is determined that the candidate partition group is within the threshold range, the method 700 proceeds to block 718 and the candidate partition group is identified as representing a partition. In some embodiments, such candidate partition groups are designated and / or stored for image normalization.

[0320] Reference now Fig.28 , a flow chart showing one embodiment of a method 800 for performing illumination-independent image normalization is shown. The method 800 may be performed by all or part of the system 100. The method 800 may be performed as Fig.23 The method 800 may be performed as part of the imaging of block 520 of the method 500. In some embodiments, the method 800 may be performed by the controller 300 and the imager 308. The method 800 may include determining, generating and / or collecting data, values ​​and / or images. In some embodiments, some or all of these data, values ​​and / or images may be stored in one or more databases in the memory 302.

[0321] The method 800 begins at box 802, where the area to be imaged is illuminated by the imager 308, and in some embodiments by the excitation source 310 in the image, and an image of the illuminated area is generated by the imager 308 and in some embodiments by the image capture device 312. The area to be imaged may include a PCR chip 234, which includes a plurality of partitions. The area to be imaged may be illuminated with some or all of the excitation frequencies, and such illumination with some or all of the excitation frequencies may be performed serially or in parallel. In some embodiments, for example, continuous illumination will include illuminating the area to be imaged with a first frequency or a first frequency range of excitation light, followed by illuminating the area to be imaged with one or several additional frequencies and / or frequency ranges of excitation light, each time with one frequency or frequency range until all desired excitations and / or imaging are completed. In some embodiments, the area to be imaged may be illuminated with broad spectrum light such as white visible light.

[0322] In some embodiments, one or several images may be generated for each frequency and / or frequency range at which the area to be imaged is irradiated. In some embodiments, one or several of these images may be generated using one or several filters to capture and / or image one or several desired frequencies and / or frequency ranges. Each of the images may contain multiple pixels.

[0323] At box 804, an image is selected and divided into a plurality of segments, each of which has the same shape and / or includes the same number of pixels. In some embodiments, each segment may include a rectangular segment with an equal number of pixels. In some embodiments, each of the segments includes some of the partitions contained on the PCR chip 234. In some embodiments, the selected image may be an aggregation of the best image and / or multiple images for each frequency and / or frequency range for generating an image. In some embodiments, for example, where multiple images are generated for each excitation frequency and / or frequency range, the selected image may be an aggregation of multiple images generated for one of the excitation frequencies and / or one of the excitation frequency ranges.

[0324] At block 806, one of the image segments is selected and portions of the selected segment corresponding to the partitions in the segment are identified. This may include identifying portions of the image corresponding to each partition in the segment. Fig. 27 These partitions are identified by the method 700. This step may be repeated until it has been performed for each segment of the image.

[0325] At block 808, a brightness value for each of the image portions corresponding to the partition is identified. In some embodiments, this brightness value may be identified by identifying a pixel value for each pixel in the image portion corresponding to the partition, which may be a highest pixel value, an average pixel value, a median pixel value, etc. This step may be repeated until brightness values ​​for all image portions corresponding to the partition have been identified.

[0326] At box 810, the brightness value of each partition is compared with a threshold value to determine whether the partition is a positive partition or a negative partition. As used herein, a positive partition is a partition with a brightness value indicating that it contains a target and / or contains more than a minimum target amount, and a negative partition is a partition with a brightness value indicating that it does not contain a target and / or contains less than a minimum target amount. Therefore, in some embodiments, a negative partition is a partition with a low signal captured in an image. Based on a comparison of the brightness value of the portion of the image corresponding to the partition with the threshold value, negative partitions in the image segment are identified, and the brightness values ​​of these negative partitions are also identified. This step can be repeated until all negative partitions in the image have been identified as having the brightness values ​​of those negative partitions.

[0327] At block 812, a segment is selected and an average brightness value corresponding to the image portion of the negative partition in the image segment is generated and / or determined. This step may be repeated so that an average brightness value corresponding to the image portion of the negative partition is generated and / or determined for each segment of the image.

[0328] At block 814, the average negative partition brightness values ​​of each of the image segments are compared and a minimum average negative partition brightness value is identified. In some embodiments, this may include identifying the segment of the image having the minimum average negative partition brightness value.

[0329] At box 816, the average negative partition brightness value of each image segment in the image segment is divided by the minimum average negative partition brightness value identified in box 814 to determine and / or generate a segment normalized value for the segment. Therefore, this normalized value for the segment is based at least in part on the average brightness value of the segment. In some embodiments, a segment is selected and the average negative partition brightness value of the segment is retrieved. The average negative partition brightness value of the segment is divided by the minimum average negative partition brightness value identified in box 814. The result of this division is to generate a segment normalized value for the selected segment. This segment normalized value can be stored in a database in, for example, memory 302.

[0330] At block 818, an image segment is selected and pixel values ​​for the image segment are retrieved. In some embodiments, these pixel values ​​may be retrieved from memory 302. This may be repeated for each segment so that pixel values ​​for each segment of the image have been retrieved. In some embodiments, these pixel values ​​may include pixel values ​​for all pixels in the selected segment, and in some embodiments, these pixel values ​​may be pixel values ​​for a portion of the image corresponding to a partition in the selected segment.

[0331] At block 820, each pixel value in the selected image segment is divided by the segment normalization value of the image segment. The pixel value divided by the normalization value of the image segment of the pixel generates a normalized pixel value. Therefore, in some embodiments, the pixel values ​​in each segment are normalized according to the normalization value of the segment. After completing step 820 for the segment, the method 800 proceeds to decision step 822, where it is determined whether there are additional segments whose pixel values ​​have not been normalized. If there are additional segments, the method 800 returns to block 818 and continues as described above. In some embodiments, and upon returning to block 818, the next image segment is selected.

[0332] Returning again to decision step 822, if it is determined that there are no additional image segments that require pixel value normalization, the method 800 proceeds to block 824 where the normalized pixel values ​​of the image segments are stored. In some embodiments, the normalized pixel values ​​of the image segments and / or the normalized pixel values ​​of the image can be stored in the memory 302, and the annotations are specifically stored in a database of the memory 302. At block 826, the image is analyzed according to the normalized pixel values ​​in some embodiments, which can include analyzing the normalized pixel values ​​of the image. In some embodiments, the image can be analyzed to determine the presence or absence of at least one target based on the normalized pixel values.

[0333] Reference now Fig.29 , a flow chart showing one embodiment of a method 900 for performing illumination-dependent image normalization is shown. The method 900 may be performed by all or part of the system 100. The method 900 may be performed as Fig.23 The method 900 may be performed as part of the imaging of block 520 of the method 500. In some embodiments, the method 900 may be performed by the controller 300 and the imager 308. The method 900 may include determining, generating and / or collecting data, values ​​and / or images. In some embodiments, some or all of these data, values ​​and / or images may be stored in one or more databases in the memory 302.

[0334] The method 900 begins at block 902, where it is determined to perform image normalization. In some embodiments, this determination can be made by a controller based on, for example, the amount of time that has passed since the last time image normalization was performed. Thus, in some embodiments, image normalization can be performed periodically, such as before or after each run.

[0335] At block 904, the imager 308 is repositioned to image the test field. In some embodiments, the test field may contain an area having a single uniform color that fills the entire image generated by the imager 308. In some embodiments, the imager 308 may be directed by the controller 300 to reposition itself to image the test field.

[0336] In block 906 , the test field is illuminated and an image of the test field is generated. In some embodiments, the test field is illuminated by imager 308 and the image of the test field is generated by imager 308 .

[0337] At frame 908, the pixel value of each pixel in the pixel in the image is identified, and at frame 910, outlier pixel values ​​are identified and removed. In some embodiments, outlier pixels can be identified by comparing with one or several threshold values ​​and / or outlier pixels can be identified statistically. In some embodiments, outlier pixels can be identified statistically by determining the standard deviation of the average pixel value and the pixel value. Outlier pixels can be pixels whose pixel values ​​differ from the average pixel value by more than a predetermined standard deviation multiple. In some embodiments, for example, outlier pixels refer to pixels whose pixel values ​​differ from the average pixel value by at least two standard deviations, whose pixel values ​​differ from the average pixel value by at least three standard deviations, or whose pixel values ​​differ from the average pixel value by any other or intermediate number of standard deviations. Once outlier pixel values ​​have been identified, those outlier pixel values ​​can be removed.

[0338] At frame 912, identify the pixel with minimum pixel value except the pixel with outlier pixel value, and identify and select the minimum pixel value of the pixel. At frame 714, generate and / or calculate normalization factor for each pixel based on minimum pixel value. In some embodiments, the generation of normalization factor of pixel includes taking the pixel value of the pixel and dividing it by minimum pixel value. In some embodiments, this can be repeated for each pixel in the pixel, so that normalization value is generated for each pixel, and in some embodiments, this can be repeated for each non-outlier pixel in non-outlier pixel, so that normalization value is generated for each non-outlier pixel in non-outlier pixel. The normalization value of each pixel can be associated with its pixel, and can be stored in the database of memory 302.

[0339] At block 916, the imager is repositioned to image the sample, specifically the PCR chip 234. In some embodiments, this may include the controller 300 generating one or more control signals to cause the imager 308 to be repositioned to image the PCR chip 234. After the imager 308 has been repositioned to image the PCR chip 234, the PCR chip 234 may be illuminated, and an image of the PCR chip 234 may be generated, as shown in block 918. The generation of the image of the PCR chip 234 may include illuminating the PCR chip 234 with excitation energy from the excitation source 310, and capturing the image of the PCR chip 234 with the image capture device 312.

[0340] At box 920, pixels and their associated pixel values ​​from the image of the PCR chip 234 are identified. The pixel value of each pixel is normalized by the normalization factor of the pixel. In some embodiments, normalizing each pixel may include selecting a pixel and identifying the normalization factor and pixel value of the pixel. The pixel value of the pixel may then be divided by the normalization factor of the pixel to generate a normalized pixel value for the pixel.

[0341] At block 922, the image is analyzed according to the normalized pixel values ​​in some embodiments, which may include analyzing the normalized pixel values ​​of the image. In some embodiments, this may include identifying negative partitions and / or positive partitions based on the normalized pixel values, and determining the presence, absence, and / or amount of the target in the sample based thereon.

[0342] Reference now Fig.30 , a flow chart showing one embodiment of a method 1000 for single layer detection is shown. The method 1000 may be performed by all or part of the system 100. The method 1000 may be used as Fig.23 520 of method 500. In some embodiments, method 1000 may be performed by controller 300 and imager 308. Method 1000 may include determining, generating and / or collecting data, values ​​and / or images. In some embodiments, some or all of these data, values ​​and / or images may be stored in one or more databases in memory 302.

[0343] In some embodiments, method 1000 may be performed as part of the steps of block 520. This may include, for example, method 700 for identifying partitions. Thus, in some embodiments, method 1000 may include identifying pixels from an image as belonging to valid droplets or to background using a machine learning model.

[0344] Method 1000 begins at block 1002, where a sample is collected and prepared for analysis. In some embodiments, this may include receiving the sample in system 100, and preparing the sample for PCR, and specifically using system 100 for performing automated digital PCR. In some embodiments, this may include steps of blocks 502 to 512 of method 500.

[0345] At box 1004, droplets of sample are generated on a substrate. The substrate can be, for example, any article configured to receive and / or hold one or more partitions, and specifically one or more droplets for thermal cycling and / or imaging. In some embodiments, the substrate can be planar, and / or can include multiple zones and / or chambers. The droplets can each have a volume between about 50 picoliters and about 300, and each droplet in the droplet can include a partition. In some embodiments, generating droplets of sample on a substrate can include generating at least 500,000 droplets of sample on a substrate. The substrate can be any surface that can receive droplets. In some embodiments, the PCR chip 234 can include a substrate.

[0346] At block 1006, the substrate, and therefore the sample, is illuminated and imaged. In some embodiments, this may include illuminating the PCR chip 234 and generating one or several images of the PCR chip 234. In some embodiments, the sample and substrate are illuminated by the imager 308, and images of the sample and substrate are generated by the imager 308.

[0347] At block 1008, the image generated in block 1006 is ingested into an artificial intelligence classifier, and specifically an image of a droplet of the sample is ingested into the artificial intelligence classifier. This artificial intelligence classifier may include a machine learning classifier. In some embodiments, the image ingested into the artificial intelligence classifier may include an image of the droplets generated on the substrate in block 1006. In some embodiments, the artificial intelligence classifier may be trained to generate an output including one or several probabilities that the droplet is a monolayer. As used herein, a droplet is a monolayer when it is not stacked on top of another droplet.

[0348] At block 1010, an output is received from the artificial intelligence classifier. In some embodiments, the output may include a plurality of probabilities. In some embodiments, each probability in the plurality of probabilities indicates a likelihood that a droplet is a monolayer. Thus, in some embodiments, the output received from the artificial intelligence classifier identifies the probability that each droplet is a monolayer droplet.

[0349] At block 1012, and for each of the droplets of the sample on the substrate, it is determined whether the droplet is a monolayer or a non-monolayer. In some embodiments, this may include iteratively selecting a droplet, retrieving a probability output by an artificial intelligence classifier and associated with the droplet, and comparing the probability to one or more thresholds. Based on the comparison of the probability to the one or more thresholds, it may be determined whether the selected droplet is a monolayer or a non-monolayer, or more specifically, whether to classify the selected droplet as a monolayer or a non-monolayer. This may be repeated until each droplet is identified as a monolayer or a non-monolayer.

[0350] At block 1014, portions of the image containing non-monolayer droplets and portions of the image containing monolayer droplets are identified. At block 1016, the non-monolayer portion of the image is excluded from the sample analysis. Thus, in some embodiments, the portion of the image containing non-monolayer droplets in block 1014 is excluded from the image analysis.

[0351] At block 1018, the total size of the monolayer regions in the image is determined. In some embodiments, this can include identifying all portions of the image that contain only monolayer droplets, determining the size of those portions of the image, and adding the sizes of those portions of the image together. At block 1020, the total size of the combined monolayer regions is compared to a threshold. In some embodiments, this threshold can delineate between the total size of the monolayer regions in the image that are sufficient to obtain a valid result and the total size of the monolayer regions in the image that are insufficient to obtain a valid result. The threshold delineating between the monolayer size that is sufficient to obtain a valid result and the monolayer size that is insufficient to obtain a valid result can be determined statistically and can indicate when the image includes an insufficient number of monolayer partitions, and specifically an insufficient number of monolayer droplets, to accurately analyze the image.

[0352] At decision step 1022, it is determined whether the total size of the combined monolayer regions in the image is sufficient to obtain a valid result. If it is determined that the total size of the combined monolayer regions is sufficient to obtain a valid result, the method 1000 proceeds to block 1024 and the monolayer regions of the image are analyzed. In some embodiments, this may include identifying negative partitions and / or positive partitions based on the normalized pixel values, and determining the presence, absence, and / or quantity of the target in the sample based thereon. In some embodiments, analyzing the image may include analyzing a portion of the image containing monolayer droplets to determine whether at least one target is present in each droplet.

[0353] Alternatively, if it is determined that the total size of the combined monolayer regions in the image is insufficient to obtain a valid result, the method 1000 proceeds to block 1026 and an alert is generated indicating an invalid test result.

[0354] Reference now Figures 29 to 40 , a screen shot of an embodiment of a graphical user interface (“GUI”) is shown. The graphical user interface can be generated by the controller 300 and can be provided to the user via the display 304. In some embodiments, the GUI can be generated on the display 304 and / or can be controlled by the controller 300 on the display 304.

[0355] Reference now Fig.31, showing a first view of a first window 1100 generated by a GUI. The first window 1100 includes a plurality of action selection buttons 1120, 1122, 1124. Each of these action selection buttons 1120, 1122, 1124 may contain a graphical icon that, when manipulated, causes the GUI to change to display a new window. These may include: a run status button 1120 that, when manipulated, causes the GUI to display a run status; a ready to run button 1122 that, when manipulated, causes the GUI to display features configured to help prepare for a run; and a run results button 1124 that, when manipulated, causes the GUI to display run result information. As can be seen, the first window 1100 is a window generated after manipulating the ready to run button 1122.

[0356] The first window 1100 further includes a create batch button 1135. The create batch button 1135 contains a graphical icon that can be manipulated by the user to request the creation of a batch for processing. This creates the batch button 1135 when manipulated by the user, causing the GUI to display information to guide the user to set up a batch for processing by the system 100.

[0357] The first window 1100 and other windows include a state identifier 1128. The state identifier may indicate the state of the system 100, and in particular the state of one or more tasks. In some embodiments, the state identifier 1128 may include one or more graphical features, each of which may depict a state through one or more processes and / or workflows.

[0358] The status identifier 1128 may include a preparation status identifier 1130 and a process status identifier 1132. The preparation status identifier 1130 may indicate the progress of completing the preparation for performing digital PCR, and the process status identifier 1132 may indicate the progress of completing the performing digital PCR. Fig.31 In the illustrated embodiment, each of these identifiers 1130, 1132 comprises a bar whose length indicates the progress toward completing the action.

[0359] The first window 1100 further includes a batch pane 1134 and a run pane 1136. The batch pane 1134 may contain a list of samples that have been entered into the system 100 for processing but have not yet been processed, and further, whose processing has not yet been scheduled. The batch pane 1134 further includes information related to the samples, such as one or more sample identifiers, reagents used to process the samples, when the samples entered the system, and a priority for processing the samples.

[0360] In some embodiments, these one or several samples may be added to a batch by manipulating the batch creation button 1135 and selecting which samples should be associated with the batch.

[0361] Run pane 1136 includes information related to one or more upcoming runs. This may further include displaying one or more scheduled upcoming runs, and / or features configured to help plan and / or schedule one or more runs.

[0362] The first window 1100 can further include a start run button 1138. In some embodiments, manipulating the start run button 1138 can include receiving a request from a user through the GUI to perform an automated digital PCR assay on a sample using the system 100.

[0363] When the batch creation button 1135 is operated, and as Fig.32 As can be seen, the GUI can generate a second window 1102 that is configured to facilitate the user to create a batch. The second window can include a batch creation pane 1140 that can include information identifying the samples included in the batch and can allow the user to select the samples to be included in the batch. The batch creation pane 1140 can include one or more user-manipulable features that are configured to enable the user to add one or more samples to the batch. Fig.32 14, these one or more features may include, for example, one or more batch drop-down menus 1142. In some embodiments, the user may select samples for inclusion in a batch, and / or select reagents for analyzing the selected samples, via the batch drop-down menu 1142. In some embodiments, and as part of selecting samples and / or reagents for inclusion in a batch, the user may be prompted to select reagents and / or scan samples or scan identification features of samples and / or reagents via the batch drop-down menu 1142.

[0364] After samples and / or reagents have been selected for inclusion in a batch, the user may actuate Create button 1144, which may cause the samples and / or reagents indicated by the user to be associated with the batch to be associated with the newly created batch.

[0365] Reference now Fig.33 , showing a second view of the first window 1100. Similar to Fig.31 In the embodiment of the present invention, the second view of the first window includes buttons 1120, 1122, 1124, a batch creation button 1135 and a batch pane 1134, and also includes a batched sample pane 1146. The batched sample pane 1146 can display the batched samples. Fig.32When a batch is created as shown, the batch can be added to a batched samples pane 1136. The batched samples can also be displayed in a run pane 1136, where the batched samples can be scheduled for a run, and / or where one or more batched samples can be selected for a run, and a run can be started and / or requested by manipulating a start run button 1138. In some embodiments, a request to perform an automated digital PCR assay can identify an assay type, reagents, and / or samples for performing the assay.

[0366] Reference now Fig.34 , showing a first view of a third window 1104 generated by the GUI. This third window may be generated after the user selects a batch and manipulates the start run button 1138. The third window may include many of the features previously discussed, and may also include an animation pane 1148 and an instruction pane 1150. In some embodiments, the instruction pane may include information in the form of one or more instructions that guide the user to set up the system 100 to prepare for performing automated digital PCR on one or more samples. In some embodiments, the animation pane 1148 may include an animation depicting how to perform and / or execute instructions from the instruction pane 1150. Specifically, the animation pane may include an animation rendering of the system 100 and the execution of any instructions in the instruction pane 1150. Therefore, in some embodiments, the GUI instructs the user to take an action, and depicts taking the action to guide the user to complete the action.

[0367] exist Fig.34 In the first view of the third window 1104, the instruction pane 1150 guides the user to enter reagents and / or samples for the run. In some embodiments, this may include guiding the user to enter information and / or select information to identify the run batch. After providing and / or entering the desired information, the user can manipulate the confirm batch button 1152.

[0368] Reference now Fig.35 , showing a second view of the third window 1104. Once the batch is confirmed and the confirm batch button 1152 has been manipulated, the third window may advance to the first instruction 1154 in the instruction pane 1150 and the first animation in the animation pane 1148. In some embodiments, the first instruction may include guiding the user to remove one or more consumables from the shelf 126. In some embodiments, the first animation in the animation pane 1148 may include an animated rendering of the system 100 and the execution of the first instruction 1154, i.e., removing one or more consumables from the shelf 126. When the user has completed the actions guided by the first instruction, the user may click the next button 1156 to advance to the next instruction.

[0369] The third window 1104, and specifically the instruction pane 1150 of the third window, may include a progress indicator 1155. The progress indicator 115 may include a graphical representation of the progress made by the user by preparing the system 100 to perform automated digital PCR on the sample. In some embodiments, the progress indicator 1155 may include a plurality of sections 1157, each of which may be associated with a step in preparing the system 100 to perform automated digital PCR on the sample. In some embodiments, each of these sections 1157 may be shown in a first color when the step has not yet begun, in a second color when the step is in progress, or in a third color when the step is completed.

[0370] Reference now Fig.36 , showing a third view of the third window 1104. Once the consumable has been removed, the third window 1104 can proceed to the second instructions 1158 in the instruction pane 1150 and the second animation in the animation pane 1148. In some embodiments, the second instructions 1158 can include guiding the user to clean the partition 126 of the system. In some embodiments, the second animation in the animation pane 1148 can include an animated rendering of the system 100 and the execution of the second instructions 1158, i.e., cleaning the partition 126. When the user has completed the actions guided by the second instructions 1158, the user can click the next button 1156 to proceed to the next instruction.

[0371] Reference now Fig.37 , showing a fourth view of the third window 1104. Once the shelf has been cleaned, the third window 1104 can proceed to the third instructions 1160 in the instruction pane 1150 and the third animation in the animation pane 1148. In some embodiments, the instruction pane 1150 can further include a graphical representation 1162 of the shelf 126 and the plurality of positions 128 in the shelf 126. In some embodiments, the graphical representation of the shelf 126 and the plurality of positions 128 indicates the positioning of the first position for receiving the first consumable of the consumable 200.

[0372] In some embodiments, the third instruction 1160 may include guiding the user to load the first consumable into the first position 128 on the shelf 126 of the system 100. In some embodiments, the third animation in the animation pane 1148 may include an animation rendering of the system 100 and the execution of the third instruction 1160, i.e., loading the first consumable into the first position 128 of the shelf 126. When the user has completed the actions guided by the third instruction 1160, the user may click the next button 1156 to advance to the next instruction.

[0373] like Fig.37As seen in the figure, the third instruction guides loading the well plate on the pre-amplification thermal cycler 130, and the graphical representation 1162 of the partition 126 indicates the location 1163 of the position for storing consumables, graphically guiding the user to properly load the well plate according to the third instruction 1160, that is, the graphical representation 1162 of the partition 126 indicates the location of the pre-amplification thermal cycler 130, graphically guiding the user to properly load the well plate according to the third instruction 1160. In some embodiments, the consumables 200 may include, for example, at least one of the following: a sample tube, a reagent cartridge, a pipette tip box, a lysis-binding plate, a DNA quantification strip, a PCR cartridge, a PCR cartridge cover, and a magnetic separation plate. In some embodiments, the lysis-binding plate may include a metal-doped polymer, and in some embodiments, the sample tube 206 may include a magnet, which may be positioned adjacent to one side of the sample tube 206.

[0374] Reference now Fig.38 , showing a fifth view of the third window 1104. Once the first consumable has been loaded into its indicated location, the third window 1104 may advance to the fourth instructions 1170 in the instruction pane 1150 and the fourth animation in the animation pane 1148. In some embodiments, the instruction pane 1150 may further include a graphical representation 1162 of the divider 126 and multiple positions 128 in the divider 126. In some embodiments, the graphical representation of the divider 126 and multiple positions 128 indicates the location of a second position for housing a second consumable 200. In some embodiments, the graphical representation 1162 further indicates the location in which the consumable 200 has been loaded, and specifically, the graphical representation of the divider has been updated to show that the consumable has been loaded into its location after receiving the following indication through the GUI: completing the execution of the previous instructions for loading those consumables. Thus, as Fig.38 As seen in , graphical representation 1162 has been updated to show the well plate loaded onto pre-amplification thermal cycler 130.

[0375] In some embodiments, the fourth instruction 1170 may include guiding the user to load a subsequent consumable into a subsequent position 1172 on the shelf 126 of the system 100. In some embodiments, the fourth animation in the animation pane 1148 may include an animation rendering of the system 100 and the execution of the fourth instruction 1160, i.e., loading a subsequent consumable into a subsequent position 1172 on the shelf 126. When the user has completed the actions guided by the fourth instruction 1170, the user may click the next button 1156 to advance to the next instruction.

[0376] like Fig.38 As seen in FIG. 1 , the fourth instructions guide loading the sample onto the partition, and the graphical representation 1162 of the partition indicates the positioning 1172 , graphically guiding the user to properly load the sample according to the fourth instructions 1170 .

[0377] In some embodiments, the GUI may repeatedly provide a fourth instruction and a fourth animation that guides the loading of one or more subsequent consumables 200 until all consumables are loaded. Therefore, in some embodiments, the third window 1104 in the GUI may be updated when the user executes the previously provided instructions. In some embodiments, this update may include updating the instruction pane to include updated instructions and / or may include updating the animation pane to include updated animation rendering of the system and execution of subsequent instructions.

[0378] Reference now Fig.39 , showing a sixth view of the third window 1104. Once the subsequent consumables have been loaded into their indicated locations, the third window 1104 may advance to the fifth instructions 1180 in the instruction pane 1150 and the fifth animation in the animation pane 1148. In some embodiments, the instruction pane 1150 may further include a graphical representation 1162 of the shelf 126 and a plurality of positions 128 in the shelf 126. As can be seen, all of the consumables 200 have been loaded, and thus the graphical representation 1162 of the shelf 126 shows all of the consumables 200 in their proper locations.

[0379] In some embodiments, the fifth instruction 1180 may include guiding the user to close the door on the system 100 and start the pre-run check. In some embodiments, the fifth animation in the animation pane 1148 may include an animation rendering of the system 100 and the execution of the fifth instruction 1160, that is, closing the door on the system and starting the pre-run check. When the user has closed the door, the user can click the pre-run check button 1182 to advance to start the pre-run check. In some embodiments, the pre-run check can be started and / or performed when the setup of the system 100 is completed. In some embodiments, performing the pre-run check may include determining that each of the consumables 200 for performing the requested assay is loaded into the correct portion on the partition 126.

[0380] Reference now Fig.40 , a fourth window 1106 generated by the GUI is shown. The fourth window 1106 may be generated as part of performing the pre-run checks. The fourth window 1106 may include an indication of successful completion of the pre-run checks 1184, a graphical representation 1162 of the bulkhead 126, a graphical representation of each consumable 200 loaded into the bulkhead 1186, and / or an indication that each of the consumables 200 was successfully loaded 1188 into the correct location 128 on the bulkhead 126. Fig.40In the embodiment of the present invention, the indication of successful loading 1188 of each of the consumables is checked. Alternatively, if one of the consumables is not successfully loaded, the GUI can display an indication that the consumable was not successfully loaded, which can include, for example, an "x".

[0381] After the user has reviewed the results of the pre-run checks, and if all consumables are loaded successfully, the user can manipulate the start run button 1190 to begin automated digital PCR.

[0382] Reference now Fig.41 , a flow chart illustrating one embodiment of a method 1200 for performing DDPCR is shown. The method 1200 may be performed using all or part of the system 100. The method 1200 begins at block 1202, where a sample is prepared according to steps 502 to 512 of the method 500. In some embodiments, this may include preparation of an assay mixture.

[0383] At block 1204, oil is transferred from the reagent cartridge 212 to the oil reservoir 284 of the droplet generation unit 282 of the droplet generator 164. In some embodiments, the reagent cartridge 212 may include one or several compartments 214 containing oil. In some embodiments, each row of compartments 214 in the reagent cartridge 212 may include one or several compartments 214 containing oil. In some embodiments, step 1204 may include transferring oil from one or several compartments 214 of the reagent cartridge 212 to the oil reservoir 284 via the pipette 150, and specifically via one or several pipette tips 222 coupled to the dispensing head 328 of the pipette 150. In some embodiments, the pipette tip 222 may include a 200 μL pipette tip 222.

[0384] In some embodiments, oil can be transferred to an oil reservoir 284 on a droplet generator 164 having the same number of droplet generation units 282 as the dispensing heads 328 on the pipette 150. For example, in an embodiment where the pipette 150 has eight dispensing heads 328, oil can be transferred from a reagent cartridge 212 having eight rows of compartments 214 to a droplet generator 164 containing eight droplet generation units 282.

[0385] At block 1206, the assay mixture may be transferred to a PCR reagent reservoir 286 of a droplet generation unit 282 of a droplet generator 164. This may include transferring the assay mixture from one or several wells of an assay strip 238 to one or several PCR reagent reservoirs 286. In some embodiments, this transfer may be performed by a pipette 150, which may include a pipette tip 222. In some embodiments, the pipette tip may include a 50 μL pipette tip 222.

[0386] In some embodiments, the assay mixture can be transferred to a PCR reagent reservoir 286 on a droplet generator 164 having the same number of droplet generation units 282 as the dispensing heads 328 on the pipette 150. For example, in embodiments where the pipette 150 has eight dispensing heads 328, the assay mixture can be transferred from an assay strip 238 to a droplet generator 164 containing eight droplet generation units 282.

[0387] At block 1208, droplets are generated using the droplet generation unit 282. In some embodiments, this may include engaging the dispensing head 328 of the pipette 150 to the droplet outlet 288. In some embodiments, this engagement between the dispensing head 238 of the pipette 150 and the droplet outlet 288 may be a sealed engagement. This engagement may be performed by the pipette 150 dispensing head 238 and the droplet outlet 288. Fig.42 As described in Fig.42 As seen in FIG, the sealing engagement may be achieved by a gasket 289 positioned at the open top of the drop outlet 288 , the gasket 289 being configured to seal with the dispensing tip 328 of the pipette 150 .

[0388] In some embodiments, the pipette 150 can generate a vacuum in each droplet outlet 288 that is sealingly coupled to the dispensing head 328, which can draw a portion of the assay mixture and / or oil through one or more channels extending through the substrate 280 of the droplet generator 164. In some embodiments, this vacuum can be maintained until all of the assay mixture in the PCR reagent reservoir 286 has been converted into droplets. In some embodiments, this can include generating approximately 10,000 droplets to 1,000,000 droplets, generating at least 10,000 droplets, generating at least 5,000 droplets, or any other or intermediate number of droplets. In some embodiments, and after generating one or more droplets, the pipette 150 can apply a positive pressure to each of the droplet outlets 288 to push some of the oil drawn into the droplet outlets 288 back into the oil reservoir 284 during the generation of the droplets, while retaining some or all of the droplets in the droplet outlets 288. Thus, in some embodiments, pushing the oil back into the oil reservoir 284 does not push any droplets out of the droplet outlet 288 .

[0389] At block 1210, a PCR chip 234 is positioned to receive the droplets generated in block 1208. In some embodiments, this PCR chip 234 may include a DDPCR chip 235 (droplet PCR chip 235). The DDPCR chip 235 may be configured to receive any desired number of droplets, including, for example, about 5,000 to about 2,000,000 droplets, about 10,000 to about 1,000,000 droplets, greater than about 10,000 droplets, greater than about 20,000 droplets, or any other or intermediate number of droplets.

[0390] In some embodiments, the DDPCR chip 235 is positioned on the chip tray 144. In some embodiments, this may include moving the DDPCR chip 235 with a pipette 150, and specifically with a suction cup 340 on the pipette 150. In some embodiments, the DDPCR chip 235 may be positioned in the chip tray 144 when the chip tray 144 is in the open position.

[0391] At block 1212, the PCR chip 234, and specifically the DDPCR chip 235, is loaded with droplets generated by the droplet generation unit 164. In some embodiments, this may include aspirating droplets from the droplet outlet 288, with one or several pipette tips 222 each coupled to one or the dispensing head 328 of the pipette 150. In some embodiments, the pipette tip 222 may be a 50 μL pipette tip 222, a 100 μL pipette tip 222, a 200 μL pipette tip 222, or any other or intermediate sized pipette tip 222.

[0392] The aspirated droplets can then be distributed into an inlet of the DDPCR chip 235, such as one or more of the inlets 264, 265, 266. In some embodiments, the droplets can flow from the inlet into one of the zones, such as into one or more of the first zone 252 or the second zone 256 of the DDPCR chip 235.

[0393] At frame 1214, the PCR chip 234, and specifically the DDPCR chip 235, is sealed. In some embodiments, this may include sealing the droplet in the DDPCR chip 235. In some embodiments, the droplet may be sealed in the PCR chip 234, and specifically the DDPCR chip 235, by sealing the inlet of the PCR chip 234, and specifically the inlet of the DDPCR chip 235. In some embodiments, the inlets may be sealed by placing a sealant in the inlet. Such a sealant may include, for example, an adhesive and / or glue, such as a UV glue. In some embodiments, an adhesive such as a UV glue may be placed in the inlet of a PCR chip 234 (such as a DDPCR chip 235) by a pipette 150. For example, in some embodiments, the pipette 150 may utilize one or more pipette tips 222 to aspirate and then dispense an adhesive such as a UV curable glue into the inlet of a PCR chip 234 such as a DDPCR chip 235. In some embodiments, these pipette tips 222 may include, for example, a 200 μL pipette tip 222. In some embodiments, dispensing an adhesive into an inlet of a PCR chip 234, such as a DDPCR chip 235, can create a closed chamber containing a droplet.

[0394] In some embodiments, after the UV glue has been dispensed into the inlet of the PCR chip 234 and specifically into the inlet of the DDPCR chip 235, the UV glue can be cured. The UV glue can be cured by one or more UV lamps that can irradiate the PCR chip 234 and specifically the DDPCR chip 235, thereby irradiating the UV glue and curing it. In some embodiments, the UV lamp can be part of the reader module 124, and specifically part of the reader module housing 140. In some embodiments, the UV lamp can be part of the reader module 124, so that when the PCR chip 234, and specifically when the DDPCR chip 235 is moved into the reader module 124, the UV glue is cured. In some embodiments, for example, the UV light can be located in the reader module 124, and specifically in the housing 140 of the reader module 124, such that the chip tray 144 moves under the UV light when the chip tray 144 moves from an open position (outside the reader module housing 140) to a closed position, in which the chip tray 144, and specifically any contents of the chip tray 144, are located inside the reader module housing 140.

[0395] In some embodiments, the UV lamp may be communicatively coupled to the controller 300 so that the controller 300 may control the UV lamp to be turned on or off. In some embodiments, the controller 300 may control the UV lamp so that the UV lamp is turned on when the chip tray 144 is moved from the open position to the closed position, thereby exposing any contents of the chip tray 144 to the UV lamp. In embodiments where the chip tray 144 contains a PCR chip 234, such as a DDPCR chip 235 having UV glue in the inlet, moving the chip tray 144 from the open position to the closed position exposes the UV glue to UV light from the UV lamp, thereby curing the UV glue.

[0396] At block 1216, the PCR chip 234, and specifically the DDPCR chip 235, is moved to the thermal cycler 306 and thermally cycled. Specifically, the thermal cycler 306 can cycle the heating and cooling of the droplets in the PCR chip 234. In some embodiments, the control signal generated by the controller 300 can control the thermal cycler 306 to control the number of cycles applied to the partitions in the PCR chip 234, control the temperature of the cycles applied to the droplets in the PCR chip 234, control the duration of the cycles applied to the droplets in the PCR chip 234, or control any other aspect of the thermal cycle of the droplets in the PCR chip 234. In some embodiments, the controller 300 can generate control signals to control the relative position of the thermal cycler 306 relative to the PCR chip 234 and / or the temperature of the PCR chip 234 and / or the droplets contained in the PCR chip 234. In some embodiments, and as part of thermal cycling, the thermal cycler 306 is brought in close proximity to the PCR chip 234, and specifically to the DDPCR chip 235, and then, while in close proximity to the PCR chip 234, the thermal cycler 306 cyclically increases and decreases the temperature of the PCR chip 234, and thereby increases and decreases the temperature of the droplets.

[0397] At box 1218, the PCR chip 234 is imaged, and the image of the PCR chip 234 is analyzed. In some embodiments where the thermal cycler 306 and the imager 308 are combined into a single module, the PCR chip 234 can be imaged without raising the thermal cycler 306. In some embodiments, imaging can include moving the imager 308 to the area of ​​interest. In some embodiments, the imager can be moved to the area of ​​interest using an autofocus or feature detection loop. After the imager 308 is in the area of ​​interest, a filter can be selected and positioned in the optical pathway. In some embodiments, this filter can be a filter in a filter wheel, and positioning the filter in the optical pathway can include rotating the filter wheel until the selected filter is positioned in the optical pathway.

[0398] After the filter has been positioned in the optical pathway, a light source such as one or more LEDs corresponding to the selected filter illuminates the droplets in the PCR chip 234. Image data of the targeted area of ​​the PCR chip 234 is captured. In some embodiments, the image data can be captured with a single channel or with multiple channels. In some embodiments, each of these channels can image different frequencies and / or frequency ranges. In some embodiments, these channels can include different frequency ranges, each of which is configured to collect different fluorescence image data. The imager 308 can then move to the next area of ​​interest, and the same imaging steps can be performed until all areas of interest are imaged.

[0399] The image data generated by the imager 308 may be passed to the controller 300 and / or CPU for processing. In some embodiments, the image data may be passed for analysis as the image data is generated, in some embodiments, the image data may be passed for analysis upon completion of certain tasks, such as completion of imaging of a target area, and in some embodiments, the image data may be passed for analysis after all image data has been generated. In some embodiments, the image data may be processed on the system 100, or may be passed to the cloud for processing. In some embodiments, the image data processing may be parallelized and / or moved to a graphics processing unit (GPU) to speed up processing and reduce processing time.

[0400] At block 1220 and after imaging is complete, the PCR chip 234 is transferred out of the reader module 124. In some embodiments, this may include moving the chip tray 144 from a closed position to an open position. In some embodiments, the PCR chip 234 may be removed from the chip tray 144 by a pipette 150 having, for example, a suction cup 340, or may be manually removed from the chip tray 144 by an operator of the system 100.

[0401] Although described in method 1200 with respect to a DDPCR method, steps 1216 through 1220 may be performed in conjunction with any other method disclosed and / or described herein.

[0402] This description should not be interpreted as implying any particular order or arrangement among or between the various steps or elements, unless the order of the various steps or the arrangement of the elements is explicitly described. Different arrangements of the components depicted in the drawings or described above, as well as components and steps not shown or described, are possible. Similarly, some features and sub-combinations are useful and can be used without reference to other features and sub-combinations. Embodiments of the present invention have been described for illustrative rather than limiting purposes, and alternative embodiments will become apparent to readers of this patent. Therefore, the present invention is not limited to the embodiments described above or depicted in the drawings, and various embodiments and modifications may be made without departing from the scope of the claims below.

Claims

1. A method for performing automated digital polymerase chain reaction (PCR), the method comprising: A sample is received in a sample tube in a sample tube holder of an automated digital PCR system, the automated digital PCR system comprising: Multichannel pipettes; a heater configured to thermally cycle the sample in the PCR cartridge; as well as Imager; performing a pipetting operation with the multichannel pipette to transfer a portion of the sample into a PCR cartridge; thermally cycling the sample in the PCR cartridge using the heater; as well as The sample in the PCR cartridge is imaged with the imager.

2. The method of claim 1, wherein the digital PCR system further comprises an assay strip comprising at least one well; the method further comprises generating a final reaction mixture in the at least one well of the assay strip, wherein at least one of the pipetting operations transfers the final reaction mixture from the at least one well of the assay strip to the PCR cartridge, wherein more than 50% of the DNA contained in the at least one well of the assay strip is contained in the PCR cartridge. 3 . The method of claim 1 , wherein performing the pipetting operation with the multichannel pipette comprises transferring multiple samples into the same PCR cartridge simultaneously.

4. A method according to claim 1, wherein the automated digital PCR system includes a partition, the partition includes a position for receiving a cartridge, wherein one of the positions for receiving a cartridge includes the sample tube holder, and wherein the pipette is capable of moving above and across the partition.

5. The method of claim 4, wherein the pipette comprises at least one pipette tip and a drip tray movable from a first position below the at least one pipette tip to a second position. 6 . The method of claim 5 , wherein performing a pipetting operation comprises moving the drip tray from the first position to the second position prior to moving the pipette across the partition.

7. The method of claim 6, wherein the drip tray remains in the second position until the pipette is positioned for aspirating or dispensing.

8. The method of claim 7, wherein the pipette comprises a plurality of suction cups coupled to the drip tray.

9. The method of claim 8, wherein the suction cup is movable from a first position to a second position, wherein the suction cup is stowed in the first position and deployed in the second position.

10. The method of claim 9, wherein the suction cup is capable of picking up and moving the PCR cartridge when the suction cup is unfolded.

11. The method of claim 10, further comprising preparing the sample for thermal cycling, wherein preparing the sample for thermal cycling comprises: lysing the sample; binding the lysed sample to magnetic beads; and The sample was pre-concentrated in the pipette tip.

12. The method of claim 11, wherein pre-concentrating the sample in the pipette tip comprises: aspirating a portion of the sample into the pipette tip, wherein nucleic acids in the sample bind to magnetic beads; positioning the pipette tip adjacent to a magnet configured to attract the magnetic beads; as well as A portion of the sample is dispensed while the pipette tip is adjacent the magnet.

13. A system for performing automated digital polymerase chain reaction (PCR), the system comprising: Multichannel pipettes; a heater configured to thermally cycle the sample in the PCR cartridge; Imager; as well as a processor communicatively coupled to each of the pipette, the heater, and the imager, wherein the processor is configured to control operation of each of the pipette, the heater, and the imager to perform digital PCR, wherein the processor is configured to: receiving an indication of receiving a sample in a sample tube within a sample tube holder of the automated digital PCR system; performing a pipetting operation with the pipette to transfer a portion of the sample into a PCR cartridge; thermally cycling the sample in the PCR cartridge using the heater; and The sample in the PCR cartridge is imaged with the imager.

14. The system of claim 13, wherein the system further comprises a partition, the partition comprising locations for receiving cartridges, wherein one of the locations for receiving cartridges comprises the sample tube holder, wherein the pipette is capable of moving over and across the partition.

15. The system of claim 14, wherein the pipette comprises at least one pipette tip and a drip tray movable from a first position below the at least one pipette tip to a second position.

16. The system of claim 15, wherein performing a pipetting operation comprises moving the drip tray from the first position to the second position prior to moving the pipette across the partition.

17. The system of claim 16, wherein the drip tray remains in the second position until the pipette is positioned for aspirating or dispensing.

18. The system of claim 17, wherein the pipette comprises a plurality of suction cups coupled to the drip tray.

19. The system of claim 18, wherein the suction cup is movable from a first position to a second position, wherein the suction cup is stowed in the first position and deployed in the second position.

20. The system of claim 19, wherein the suction cup is capable of picking up and moving the PCR cartridge when the suction cup is unfolded.

21. The system of claim 20, wherein the processor is further configured to control preparing the sample for thermal cycling, wherein preparing the sample for thermal cycling comprises: lysing the sample; binding the lysed sample to magnetic beads; and The sample was pre-concentrated in the pipette tip.

22. The system of claim 21, wherein pre-concentrating the sample in the pipette tip comprises: aspirating a portion of the sample into the pipette tip, wherein nucleic acids in the sample bind to magnetic beads; positioning the pipette tip adjacent to a magnet configured to attract the magnetic beads; as well as A portion of the sample is dispensed while the pipette tip is adjacent the magnet.

23. A method for automatic image normalization, the method comprising: generating an image of the irradiated area comprising a plurality of partitions on the PCR chip, each of the partitions comprising an assay mixture, the image comprising a plurality of pixels; identifying pixels from the image as belonging to a valid partition or to background using a machine learning model; Dividing the image into a plurality of segments, each segment containing a plurality of pixels; generating average brightness values ​​for at least some of the partitions in each segment; generating a normalized value for each segment, the normalized value based at least in part on the average brightness value for the segment; normalizing pixel values ​​in each segment according to the normalization value of the segment; as well as The image is analyzed based on the normalized pixel values ​​to determine the presence or absence of at least one target.

24. The method of claim 23, wherein each segment of the plurality of segments contains the same number of pixels.

25. The method of claim 23, further comprising: for each partition in each section, identifying the portion of the image corresponding to the partition; and A brightness value of each of the image portions is identified.

26. The method of claim 25, further comprising identifying luminance values ​​corresponding to negative partitions in each of the segments. The method of claim 26 , wherein a negative partition is a partition having a low signal captured in the image.

28. The method of claim 26, wherein generating the average luminance value for at least some of the partitions in each segment comprises generating an average negative partition luminance value for the negative partitions in each segment.

29. The method of claim 28, further comprising: comparing the average negative partition brightness values ​​for each of the segments; and identifying a minimum average negative partition brightness value.

30. The method of claim 29, wherein generating the normalized value for each segment comprises, for each segment: retrieving the negative partition luminance value for the segment; and dividing the negative partition luminance value by the minimum average negative partition luminance value.

31. The method of claim 30, wherein normalizing pixel values ​​in the segments according to the normalization value for each segment comprises, for each pixel value in the segment: retrieving the pixel value; and dividing the pixel value by the normalization value.

32. The method of claim 31 , wherein identifying pixels from the image as belonging to a valid partition or to background using the machine learning model comprises: Select pixels; Use a machine learning model to predict the probability that the selected pixel belongs to a partition; Based on a comparison of the predicted probability of the one or several pixels with a threshold, identifying those one or several pixels as belonging to a candidate partition; comparing each candidate partition to a series of thresholds; and When the size of a candidate partition is within an acceptable range defined by the series of thresholds, the candidate partition is identified as a partition.

33. A system for performing image normalization as part of an automated digital polymerase chain reaction (PCR), the system comprising: Multichannel pipettes; a heater configured to thermally cycle the sample in the PCR cartridge; Imager; as well as a processor communicatively coupled to each of the pipette, the heater, and the imager, wherein the processor is configured to: generating an image of the irradiated area comprising a plurality of subareas, the image comprising a plurality of pixels; identifying pixels from the image as belonging to a valid partition or to background using a machine learning model; Dividing the image into a plurality of segments, each segment containing a plurality of pixels; generating average brightness values ​​for at least some of the partitions in each segment; generating a normalized value for each segment, the normalized value based at least in part on the average brightness value for the segment; normalizing pixel values ​​in each segment according to the normalization value of the segment; and The image is analyzed based on the normalized pixel values ​​to determine the presence or absence of at least one target.

34. The system of claim 33, wherein each segment of the plurality of segments contains the same number of pixels.

35. The system of claim 33, wherein the processor is further configured to: for each partition in each section, identifying the portion of the image corresponding to the partition; and A brightness value of each of the image portions is identified.

36. The system of claim 35, wherein the processor is further configured to identify brightness values ​​corresponding to negative partitions in each of the segments.

37. The system of claim 36, wherein each negative partition has a low signal captured in the image.

38. The system of claim 37, wherein generating the average brightness value for at least some of the partitions in each segment comprises generating an average negative partition brightness value for the negative partitions in each segment.

39. The system of claim 38, wherein the processor is further configured to: comparing the average negative subregional luminance values ​​for each of the segments; and Identify the minimum mean negative partition brightness value.

40. The system of claim 39, wherein generating the normalized value for each segment comprises, for each segment: retrieving the negative subarea brightness value for the segment; and Divide the negative subarea brightness value by the minimum average negative subarea brightness value.

41. The system of claim 40, wherein normalizing pixel values ​​in a segment according to the normalized value for each segment comprises, for each pixel value in the segment: retrieving the pixel value; and The pixel value is divided by the normalized value.

42. The system of claim 41, wherein identifying pixels from the image as belonging to a valid partition or to background using the machine learning model comprises: Select pixels; Use a machine learning model to predict the probability that the selected pixel belongs to a partition; Based on a comparison of the predicted probability of the one or several pixels with a threshold, identifying those one or several pixels as belonging to a candidate partition; comparing each candidate partition to a series of thresholds; and When the size of a candidate partition is within an acceptable range defined by the series of thresholds, the candidate partition is identified as a partition.

43. A method for detecting a monolayer of droplets on a PCR chip, the method comprising: generating droplets of the sample on a substrate; generating an image of a plurality of droplets on a substrate; For each droplet, determining using an artificial intelligence classifier whether the droplet is a monolayer; and The portion of the image containing the monolayer of droplets is analyzed to determine whether at least one target is present in each droplet.

44. The method of claim 43, further comprising: receiving the sample; and The samples were prepared for PCR.

45. The method of claim 44, wherein each of the droplets comprises a volume between about 10 picoliters and about 1000 picoliters.

46. ​​The method of claim 44, wherein generating droplets of the sample on the substrate comprises generating at least 500,000 droplets of the sample on the substrate.

47. The method of claim 44, wherein the image comprises a plurality of pixels, the method further comprising identifying pixels from the image as belonging to valid droplets or to background using a machine learning model.

48. The method of claim 47, wherein for each droplet, determining with the artificial intelligence classifier whether the droplet is a monolayer comprises: capturing the image of the droplets of the sample into the artificial intelligence classifier; and receiving an output from the artificial intelligence classifier, the output identifying the probability of each droplet being a monolayer droplet.

49. The method of claim 48, wherein for each droplet, determining with the artificial intelligence classifier whether the droplet is a monolayer further comprises, for each droplet, comparing the output of the artificial intelligence classifier to a threshold.

50. The method of claim 49, further comprising: identifying portions of the image containing non-monolayer droplets; identifying portions containing monolayer droplets; and excluding the identified portions based on sample analysis.

51. The method of claim 50, further comprising: determining a total size of the portion containing a monolayer of droplets, wherein the total size is determined by combining the size of each portion in the portion containing a monolayer of droplets; and comparing the total size of the portion containing a monolayer of droplets to a threshold value.

52. The method of claim 51, wherein when the total size of the portion containing the monolayer of droplets is less than the threshold, an alarm is generated indicating an invalid test result.

53. A system for performing monolayer detection as part of an automated digital polymerase chain reaction (PCR), the system comprising: Base material; Multichannel pipettes; Imager; as well as a processor communicatively coupled to each of the pipette and the imager, wherein the processor is configured to: Using the pipette, generate a droplet of the sample on the substrate; generating an image of a plurality of droplets on a substrate with the imager; For each droplet, determining whether the droplet is a monolayer using an artificial intelligence classifier; and The portion of the image containing the monolayer of droplets is analyzed to determine whether at least one target is present in each droplet.

54. The system of claim 53, wherein the processor is further configured to: receive instructions for the receipt of samples; and The samples were prepared for PCR.

55. The system of claim 54, wherein each of the droplets comprises a volume between approximately 10 picoliters and approximately 1000 picoliters.

56. The system of claim 54, wherein generating droplets of the sample on the substrate comprises generating at least 500,000 droplets of the sample on the substrate.

57. The system of claim 54, wherein the image comprises a plurality of pixels, wherein the processor is further configured to identify pixels from the image as belonging to valid droplets or to background using a machine learning model.

58. A system according to claim 57, wherein for each droplet, determining whether the droplet is a monolayer using the artificial intelligence classifier comprises: capturing the image of the droplets of the sample into the artificial intelligence classifier; and receiving an output from the artificial intelligence classifier, the output identifying the probability of each droplet being a monolayer droplet.

59. The system of claim 58, wherein for each droplet, determining with the artificial intelligence classifier whether the droplet is a monolayer further comprises, for each droplet, comparing the output of the artificial intelligence classifier to a threshold.

60. The system of claim 59, wherein the processor is further configured to: identify portions of the image containing non-monolayer droplets; identify portions containing monolayer droplets; and exclude the identified portions based on sample analysis.

61. A system according to claim 60, wherein the processor is further configured to: determine a total size of the portion containing a monolayer of droplets, wherein the total size is determined by combining the size of each portion in the portion containing a monolayer of droplets; and compare the total size of the portion containing a monolayer of droplets to a threshold value.

62. The system of claim 61, wherein when the total size of the portion containing the monolayer of droplets is less than the threshold, the processor is configured to generate an alarm indicating an invalid test result.

63. A method for pre-concentrating nucleic acids in a sample in a pipette tip of an apparatus for performing automated digital polymerase chain reaction (PCR), the method comprising: A first sample is received in a sample tube in a sample tube holder of an automated digital PCR system, the automated digital PCR system comprising: Multichannel pipettes; a heater configured to thermally cycle the sample in the PCR cartridge; as well as Imager; aspirating a first sample comprising nucleic acids into a pipette tip of the pipette, wherein the nucleic acids in the first sample bind to magnetic beads; positioning the pipette tip of the pipette adjacent to a magnet, whereby the magnetic beads are attracted to the magnet; pre-concentrating the nucleic acids of the first sample bound to the magnetic beads in the pipette tip by dispensing a portion of the first sample when the pipette tip is adjacent to the magnet, wherein the attracting of the magnetic beads to the magnet retains the magnetic beads in an undispensed portion of the first sample; concentrating the nucleic acid of the first sample bound to the magnetic beads in the wells of a magnet plate; thermally cycling the nucleic acid of the first sample in the PCR cartridge using the heater; as well as The nucleic acid of the first sample in the PCR cartridge is imaged with the imager.

64. The method of claim 63, wherein the magnet comprises a magnet located in a side of a sample tube, and wherein the dispensed portion of the first sample is dispensed in the sample tube.

65. The method of claim 64, wherein the pipette tip comprises a proximal end and a distal end, wherein the pipette tip is positioned adjacent to the magnet such that the magnet is located intermediate the proximal end and the distal end of the pipette tip.

66. The method of claim 65, wherein the portion of the first sample dispensed while the pipette tip is adjacent the magnet comprises approximately 90% of the aspirated first sample.

67. The method of claim 65, wherein the portion of the first sample dispensed while the pipette tip is adjacent the magnet comprises between about 50% and about 95% of the aspirated first sample.

68. A method according to claim 67, wherein when dispensing the portion of the first sample, the pipette tip is positioned adjacent to the magnet so that the distal end of the pipette tip extends below the magnet and into the sample tube, and so that the first sample in the pipette extends above the magnet.

69. The method of claim 68, wherein after completing the dispensing of the portion of the first sample, the first sample extends above the magnet.

70. The method of claim 69, further comprising dispensing the remaining portion of the first sample into wells in a magnet plate, the wells in the magnet plate being exposed to a magnetic field that attracts the magnetic beads and holds them within the wells.

71. The method of claim 70, further comprising: concentrating the magnetic beads of the second sample in the pipette tip by dispensing a portion of the second sample when the pipette tip is adjacent to the magnet, wherein attracting the magnetic beads to the magnet retains the magnetic beads in an undispensed portion of the second sample; and The remainder of the second sample is dispensed into the wells in the magnet plate.

72. The method of claim 71, further comprising aspirating the first sample and the remaining portion of the second sample from the holes in the magnet plate, wherein the magnetic field retains the magnetic beads within the holes.

73. A system for pre-concentrating nucleic acids in an automated digital polymerase chain reaction (PCR), the system comprising: Multichannel pipettes; Sample tube; a magnet plate comprising a plurality of holes; a partition plate, the partition plate comprising a position for receiving the sample tube and the magnet plate; Imager; as well as a processor communicatively coupled to the pipette, wherein the processor is configured to control operation of the pipette and the imager to perform digital PCR, wherein the processor is configured to: receiving an indication to receive a first sample in the sample tube, the sample tube being located within the location of the partition for receiving the sample tube; aspirating a first sample containing nucleic acid into a pipette tip of the pipette using the pipette, wherein the nucleic acid in the first sample binds to the magnetic beads; positioning the pipette tip of the pipette adjacent to a magnet, whereby the magnetic beads are attracted to the magnet; concentrating the magnetic beads of the first sample in the pipette tip by dispensing a portion of the first sample when the pipette tip is adjacent to the magnet, wherein the attracting of the magnetic beads to the magnet retains the magnetic beads in an undispensed portion of the first sample; thermally cycling the nucleic acid of the first sample in a PCR cartridge; and The nucleic acid of the first sample in the PCR cartridge is imaged with the imager.

74. The system of claim 73, wherein the magnet comprises a magnet located in a side of the sample tube, and wherein the dispensed portion of the first sample is dispensed in the sample tube.

75. The system of claim 74, wherein the pipette tip comprises a proximal end and a distal end, wherein the pipette tip is positioned adjacent to the magnet such that the magnet is located intermediate the proximal end and the distal end of the pipette tip.

76. The system of claim 75, wherein the portion of the first sample dispensed while the pipette tip is adjacent the magnet comprises approximately 90% of the aspirated first sample.

77. The system of claim 75, wherein the portion of the first sample dispensed while the pipette tip is adjacent the magnet comprises between about 50% and about 95% of the aspirated first sample.

78. A system according to claim 77, wherein when dispensing the portion of the first sample, the pipette tip is positioned adjacent to the magnet so that the distal end of the pipette tip extends below the magnet and into the sample tube, and so that the first sample in the pipette extends above the magnet.

79. The system of claim 78, wherein upon completion of the dispensing of the portion of the first sample, the first sample extends above the magnet.

80. A system according to claim 79, wherein the processor is further configured to dispense the remaining portion of the first sample into one of the plurality of holes in the magnet plate, wherein the one of the plurality of holes in the magnet plate is exposed to a magnetic field, which attracts the magnetic beads and retains the magnetic beads within the one of the plurality of holes.

81. The system of claim 80, wherein the processor is further configured to: concentrating the magnetic beads of the second sample in the pipette tip by dispensing a portion of the second sample when the pipette tip is adjacent to the magnet, wherein attracting the magnetic beads to the magnet retains the magnetic beads in an undispensed portion of the second sample; and The remaining portion of the second sample is dispensed into the one of the plurality of wells in the magnet plate.

82. A system according to claim 81, wherein the processor is further configured to aspirate the first sample and the remaining portion of the second sample from the one of the multiple holes in the magnet plate with the pipette, wherein the magnetic field holds the magnetic beads within the one of the multiple holes.

83. A system for automated digital polymerase chain reaction (PCR), the system comprising: case; a partition including a location for receiving a cartridge used in the digital PCR, the partition being located within the housing; and A multi-channel pipette capable of moving over and across the partition, the multi-channel pipette comprising: a pipette body movable over and across the diaphragm; as well as A pipette assembly coupled to the pipette body and movable relative to the pipette body, wherein the pipette assembly is movable from a first position at a first vertical distance relative to the diaphragm to a second position at a second vertical distance relative to the diaphragm, the pipette assembly comprising: a plurality of dispensing heads, each dispensing head configured to matingly engage with and fluidly couple to a pipette tip; as well as A drip plate assembly is movable relative to both the pipette body and the pipette assembly, wherein the drip plate is automatically deployable between the pipette tip coupled to one of the dispense heads and the diaphragm.

84. The system of claim 83, wherein the drip tray includes a receiving area configured to receive an absorbent pad.

85. The system of claim 84, wherein the absorbent pad is disposable.

86. The system of claim 84, wherein the pipette assembly comprises eight dispensing heads.

87. The system of claim 84, further comprising a z-motor coupled to the pipette assembly, wherein the pipette assembly is movable relative to the pipette body by the z-motor.

88. The system of claim 87, further comprising a drip plate z-motor, wherein the drip plate assembly is movable relative to both the pipette body and the pipette assembly by the drip plate z-motor.

89. The system of claim 88, wherein the drip tray assembly comprises: vertical displacement members; and A drip pan is pivotally coupled to a bottom end of the vertical displacement member.

90. The system of claim 89, wherein the drip tray assembly further comprises an actuation member having a first end and a second end, wherein the first end of the actuation member is pivotally coupled to the drip tray, and wherein the second end of the actuation member is slidably coupled to the drip tray assembly.

91. A system according to claim 90, wherein the actuating member is configured to deploy the drip tray between the pipette tip coupled to the dispensing head and the partition when the drip tray assembly is moved to a deployed position, wherein the deployed position is defined relative to the pipette assembly.

92. The system of claim 91, wherein the drip tray assembly further comprises a plurality of suction cups.

93. The system of claim 92, wherein the suction cup is coupled to the vertical displacement member.

94. The system of claim 93, wherein the suction cup deploys when the drip tray deploys.

95. The system of claim 94, wherein when the suction cup is deployed, at least a portion of the suction cup extends below the drip tray.

96. The system of claim 95, further comprising a suction pump fluidly connected to the suction cup and configured to create a vacuum in the suction cup.

97. The system of claim 95, further comprising a controller configured to control operation of the z-motor, the drip pan z-motor, and the suction pump.

98. A method of performing automated digital polymerase chain reaction (PCR), the method comprising: Receive the sample tube in a sample tube holder in a partition of the automated digital PCR system; moving a pipette tip coupled to a pipette toward the septum to insert the pipette tip into the sample tube; aspirating a portion of the sample from the sample tube into the pipette tip coupled to the pipette; moving the pipette tip away from the septum to retract the pipette tip from the sample tube; automatically deploying a drip tray between the pipette tip and the diaphragm; creating a plurality of partitions on a PCR chip, wherein at least a portion of the sample is contained in the pipette tip; as well as The plurality of partitions are thermally cycled and imaged.

99. The method of claim 98, wherein the pipette comprises: a pipette body movable over and across the diaphragm; and A pipette assembly coupled to the pipette body and capable of moving relative to the pipette body, wherein the pipette assembly is capable of moving from a first position at a first vertical distance relative to the partition to a second position at a second vertical distance relative to the partition, the pipette assembly including a plurality of dispensing heads, each of the dispensing heads being configured to cooperatively engage with a pipette tip and fluidly coupled to the pipette tip.

100. The method of claim 99, wherein the pipette comprises a drip plate assembly movable relative to both the pipette body and the pipette assembly, the drip plate assembly comprising: vertical displacement members; and A drip pan is pivotally coupled to a bottom end of the vertical displacement member.

101. The method of claim 100, the drip tray assembly further comprising a suction cup coupled to the vertical displacement member.

102. The method of claim 101, further comprising: Move the pipette body over the partition and across the partition to above the PCR chip; moving the drip plate assembly toward the partition until the suction cup engages with the PCR chip; controlling the suction pump to generate a vacuum with the suction cup, thereby coupling the PCR chip; While maintaining the coupling to the PCR chip, moving the drip tray assembly away from the partition; While maintaining the coupling to the PCR chip, the pipette body is moved over the partition and across the partition to the chip tray; Positioning the PCR chip in the chip tray; as well as The suction pump is controlled to release the PCR chip from the suction cup.

103. A method of performing automated digital polymerase chain reaction (PCR), the method comprising: generating a graphical user interface ("GUI") on a screen of a system for automated digital PCR; receiving, by the GUI, a request to perform an automated digital PCR assay on a sample using the system for automated digital PCR; A first window is generated in the GUI, wherein the first window is configured to guide a user to set up the system for automated digital PCR, and the first window includes: A first pane, the first pane comprising: first instructions for loading a first consumable into a first position on a shelf of the system for automated digital PCR, the shelf comprising a plurality of positions; as well as a graphical representation of the divider and the plurality of positions, the graphical representation of the divider and the plurality of positions indicating positioning of the first position for receiving the first consumable product; as well as a second pane including an animated rendering of the system for automated digital PCR and execution of the first instruction; as well as Upon receiving an indication of completion of execution of the first instruction for loading the first consumable, the graphical representation of the shelf is updated to show the first consumable loaded into the first location.

104. The method of claim 103, wherein the first consumable comprises at least one of: Sample tube; Reagent cartridges; Tip Box; Lysis binding plate; DNA quantification strips; PCR cartridge; PCR cartridge cap; and Magnetic separation plate.

105. The method of claim 104, wherein the cleavage bonding plate comprises a metal-doped polymer.

106. The method of claim 104, wherein the sample tube comprises a magnet.

107. The method of claim 103, wherein the request for performing the automated digital PCR assay identifies an assay type and reagents for performing the assay.

108. The method of claim 103, wherein the first window in the GUI is updated when the user executes a first instruction previously provided.

109. The method of claim 108, wherein updating the first window in the GUI comprises: updating the first pane to include second instructions for loading a second consumable into a second location on the shelf of the system for automated digital PCR; and The graphical representation of the divider and the plurality of positions is updated to indicate the positioning of the second position for receiving the second consumable product.

110. The method of claim 109, wherein updating the first window in the GUI further comprises updating the second pane to include the animation rendering of the system for automated digital PCR and the execution of the second instruction.

111. The method of claim 110, further comprising performing a pre-run check after completing the setup of the system for automated digital PCR.

112. The method of claim 111, wherein performing the pre-run check comprises determining that each of the consumables used to perform the requested assay is loaded into a correct position on the partition.

113. The method of claim 112, wherein performing the pre-flight check further comprises generating a second window, the second window comprising: an indication of successful completion of said pre-operational checks; a graphical representation of the partition of the system for automated digital PCR; a graphical representation of each consumable loaded into the bulkhead; and An indication of successful loading of each of the consumables into the correct position on the partition.

114. The method of claim 113, further comprising generating a graphical indication of progress toward completion of the requested determination.

115. The method of claim 114, further comprising, and prior to generating the first window including the first instruction and the graphical representation: updating the first pane to include third instructions for removing one or more consumables from the shelf; and The second pane is updated to include an animated rendering of the system for automated digital PCR and removing the one or more consumables from the shelf in accordance with the third instructions.

116. A system for performing automated digital polymerase chain reaction (PCR), the system comprising: case; a partition located within the housing and comprising a plurality of locations for receiving consumables; Multichannel pipettes; Screen; as well as a processor communicatively coupled to each of the pipette and the screen, wherein the processor is configured to: generating a graphical user interface ("GUI") on said screen; receiving, via the GUI, a request to perform an automated digital PCR assay on a sample; A first window is generated in the GUI, wherein the first window is configured to guide a user to set up the system, the first window comprising: A first pane, the first pane comprising: first instructions for loading a first consumable into a first position on the shelf; and a graphical representation of the divider and the plurality of positions, the graphical representation of the divider and the plurality of positions indicating the positioning of the first position for receiving the first consumable product; and a second pane including an animated rendering of the system for automated digital PCR and execution of the first instructions; and Upon receiving an indication of completion of execution of the first instruction for loading the first consumable, the graphical representation of the shelf is updated to show the first consumable loaded into the first location.

117. The system of claim 116, wherein when the user executes a first instruction previously provided, the first window in the GUI is updated, wherein updating the first window in the GUI comprises: updating the first pane to include second instructions for loading a second consumable into a second location on the shelf; and The graphical representation of the divider and the plurality of positions is updated to indicate the positioning of the second position for receiving the second consumable product.

118. The system of claim 117, wherein updating the first window in the GUI further comprises updating the second pane to include the animation rendering of the system and the execution of the second instruction.

119. The system of claim 118, wherein the processor is further configured to perform a pre-operation check after completing the setup of the system.

120. The system of claim 119, wherein performing the pre-run check comprises determining that each of the consumables for performing the requested assay is loaded into a correct position on the partition.

121. The system of claim 120, wherein performing the pre-operational check further comprises generating a second window, the second window comprising: an indication of successful completion of said pre-operational checks; a graphical representation of said partition of said system; a graphical representation of each consumable loaded into the bulkhead; and An indication of successful loading of each of the consumables into the correct position on the partition.

122. The system of claim 121, wherein the processor is further configured to, prior to generating the first window including the first instruction and the graphical representation: updating the first pane to include third instructions for removing one or more consumables from the shelf; and The second pane is updated to include an animated rendering of the system for automated digital PCR and removing the one or more consumables from the shelf in accordance with the third instructions.

123. A method of performing automated digital droplet polymerase chain reaction (DDPCR), the method comprising: A sample is received in a sample tube in a sample tube holder of an automated digital PCR system, the automated digital PCR system comprising: Multichannel pipettes; a heater configured to thermally cycle the sample in the PCR cartridge; as well as Imager; generating droplets of a portion of the sample with a droplet generator; performing a pipetting operation with the multichannel pipette to transfer the droplets into a PCR cartridge; thermally cycling the sample in the PCR cartridge using the heater; as well as The sample in the PCR cartridge is imaged with the imager.

124. The method of claim 123, wherein the droplet generator comprises a substrate and a plurality of droplet generating units, each of the droplet generating units being located on the substrate.

125. The method of claim 124, wherein each of the droplet generation units comprises: an oil reservoir; a PCR reagent reservoir; and a droplet outlet.

126. The method of claim 125, wherein each of the oil reservoir, the PCR reagent reservoir, and the droplet outlet are fluidly coupled by at least one channel extending through the substrate.

127. A method according to claim 126, wherein generating droplets includes: engaging the multi-channel pipette with the droplet outlet of each droplet generating unit of the droplet generator; and applying a vacuum to the droplet outlet of each droplet generating unit of the droplet generator with the multi-channel pipette.

128. A method according to claim 127, wherein performing the pipetting operation to transfer the droplets to the PCR cartridge includes aspirating the droplets from the droplet outlet of each droplet generating unit of the droplet generator; and dispensing the aspirated droplets into the inlet of the PCR cartridge.

129. The method of claim 128, further comprising sealing the PCR cartridge, thereby sealing the droplet within the PCR cartridge.

130. The method of claim 129, wherein sealing the PCR cartridge comprises dispensing a sealant into the inlet of the PCR cartridge.

131. The method of claim 130, wherein the sealant comprises an ultraviolet ("UV") curable glue.

132. The method of claim 131, further comprising curing the UV curable glue prior to thermal cycling the sample in the PCR cartridge.

133. The method of claim 132, wherein imaging the sample in the PCR cartridge with the imager comprises: moving the imager to a region of interest; irradiating the PCR cartridge; positioning the filter in the optical pathway; and An image of the region of interest is captured.

134. The method of claim 133, wherein the region of interest is selected using autofocus.

135. A system for performing automated digital droplet polymerase chain reaction (DDPCR), the system comprising: Multichannel pipettes; a heater configured to thermally cycle the sample in the PCR cartridge; Imager; as well as a processor communicatively coupled to each of the pipette, the heater, and the imager, wherein the processor is configured to control operation of each of the pipette, the heater, and the imager to perform digital PCR, wherein the processor is configured to: receiving an indication of receiving a sample in a sample tube within a sample tube holder of the automated digital PCR system; generating droplets comprising a portion of the sample with a droplet generator; performing a pipetting operation with the pipette to transfer a portion of the sample into a PCR cartridge; thermally cycling the sample in the PCR cartridge using the heater; and The sample in the PCR cartridge is imaged with the imager.

136. A system according to claim 135, wherein the system further comprises a partition, the partition comprising positions for receiving cartridges, wherein one of the positions for receiving cartridges comprises the sample tube holder, and wherein the pipette is capable of moving above and across the partition.

137. The system of claim 136, wherein the droplet generator comprises a substrate and a plurality of droplet generating units, each of the droplet generating units being located on the substrate.

138. The system of claim 137, wherein each of the droplet generation units comprises: an oil reservoir; a PCR reagent reservoir; and a droplet outlet.

139. The system of claim 138, wherein each of the oil reservoir, the PCR reagent reservoir, and the droplet outlet are fluidly coupled by at least one channel extending through the substrate.

140. The system of claim 139, wherein generating droplets comprises: engaging the multi-channel pipette with the droplet outlet of each droplet generating unit of the droplet generator; and applying a vacuum to the droplet outlet of each droplet generating unit of the droplet generator using the multi-channel pipette.

141. The system of claim 140, wherein the pipette comprises at least one pipette tip and a drip tray movable from a first position below the at least one pipette tip to a second position.

142. The system of claim 141, further comprising a reader module comprising the imager and an ultraviolet ("UV") lamp.

143. The system of claim 142, wherein the processor is further configured to: controlling the multichannel pipette to dispense ultraviolet ("UV") glue in the inlet of the PCR cartridge; and The UV lamp is controlled to cure the UV glue in the inlet of the PCR cartridge.

144. The system of claim 143, wherein the reader module comprises a chip tray configured to receive the PCR cartridge and move the PCR cartridge into the reader module.

145. A system according to claim 144, wherein the reader module includes a housing and wherein a UV lamp is located on the housing so that when the PCR cartridge is moved from the chip tray into the reader module, the UV glue is exposed to the UV lamp.

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